chr2-107992192-A-G

Position:

chr2-107992192-A-G

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBA1

The NM_021815.5(SLC5A7):c.265A>G(p.Ile89Val) variant causes a missense change. The variant allele was found at a frequency of 0.0844 in 1,612,352 control chromosomes in the GnomAD database, including 6,649 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I89T) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.075 ( 582 hom., cov: 32)

Exomes 𝑓: 0.085 ( 6067 hom. )

Consequence

SLC5A7
NM_021815.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 5.23

Variant links:

Genes affected

SLC5A7 (HGNC:14025): (solute carrier family 5 member 7) This gene encodes a sodium ion- and chloride ion-dependent high-affinity transporter that mediates choline uptake for acetylcholine synthesis in cholinergic neurons. The protein transports choline from the extracellular space into presynaptic terminals for synthesis into acetylcholine. Increased choline uptake results from increased density of this protein in synaptosomal plasma membranes in response to depolarization of cholinergic terminals. Dysfunction of cholinergic signaling has been implicated in various disorders including depression, attention-deficit disorder, and schizophrenia. An allelic variant of this gene is associated with autosomal dominant distal hereditary motor neuronopathy type VIIA. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]

SLC5A7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

PM1

In a mutagenesis_site Only 20% of wild-type choline uptake activity. (size 0) in uniprot entity SC5A7_HUMAN

BP4

Computational evidence support a benign effect (MetaRNN=0.002653569).

BP6

Variant 2-107992192-A-G is Benign according to our data. Variant chr2-107992192-A-G is described in ClinVar as [Benign]. Clinvar id is 261428.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-107992192-A-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC5A7	NM_021815.5 linkuse as main transcript	c.265A>G	p.Ile89Val	missense_variant	3/9	ENST00000264047.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC5A7	ENST00000264047.3 linkuse as main transcript	c.265A>G	p.Ile89Val	missense_variant	3/9	1	NM_021815.5	P1
SLC5A7	ENST00000409059.5 linkuse as main transcript	c.265A>G	p.Ile89Val	missense_variant	3/9	1		P1

Frequencies

GnomAD3 genomes

AF:

0.0750

AC:

11415

AN:

152192

Hom.:

578

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0266

Gnomad AMI

AF:

0.0822

Gnomad AMR

AF:

0.146

Gnomad ASJ

AF:

0.0487

Gnomad EAS

AF:

0.126

Gnomad SAS

AF:

0.0331

Gnomad FIN

AF:

0.116

Gnomad MID

AF:

0.0191

Gnomad NFE

AF:

0.0829

Gnomad OTH

AF:

0.0628

GnomAD3 exomes

AF:

0.0926

AC:

23270

AN:

251232

Hom.:

1482

AF XY:

0.0865

AC XY:

11750

AN XY:

135816

show subpopulations

Gnomad AFR exome

AF:

0.0241

Gnomad AMR exome

AF:

0.204

Gnomad ASJ exome

AF:

0.0517

Gnomad EAS exome

AF:

0.124

Gnomad SAS exome

AF:

0.0288

Gnomad FIN exome

AF:

0.119

Gnomad NFE exome

AF:

0.0798

Gnomad OTH exome

AF:

0.0842

GnomAD4 exome

AF:

0.0854

AC:

124643

AN:

1460042

Hom.:

6067

Cov.:

AF XY:

0.0834

AC XY:

60568

AN XY:

726466

show subpopulations

Gnomad4 AFR exome

AF:

0.0231

Gnomad4 AMR exome

AF:

0.200

Gnomad4 ASJ exome

AF:

0.0506

Gnomad4 EAS exome

AF:

0.127

Gnomad4 SAS exome

AF:

0.0286

Gnomad4 FIN exome

AF:

0.115

Gnomad4 NFE exome

AF:

0.0858

Gnomad4 OTH exome

AF:

0.0756

GnomAD4 genome

AF:

0.0750

AC:

11421

AN:

152310

Hom.:

582

Cov.:

AF XY:

0.0767

AC XY:

5711

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.0265

Gnomad4 AMR

AF:

0.147

Gnomad4 ASJ

AF:

0.0487

Gnomad4 EAS

AF:

0.126

Gnomad4 SAS

AF:

0.0329

Gnomad4 FIN

AF:

0.116

Gnomad4 NFE

AF:

0.0829

Gnomad4 OTH

AF:

0.0621

Alfa

AF:

0.0778

Hom.:

642

Bravo

AF:

0.0778

TwinsUK

AF:

0.0868

AC:

322

ALSPAC

AF:

0.0960

AC:

370

ESP6500AA

AF:

0.0286

AC:

126

ESP6500EA

AF:

0.0814

AC:

700

ExAC

AF:

0.0839

AC:

10192

Asia WGS

AF:

0.0740

AC:

258

AN:

3478

EpiCase

AF:

0.0776

EpiControl

AF:

0.0687

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 22, 2023	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 11, 2018	This variant is associated with the following publications: (PMID: 12237312) -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Neuronopathy, distal hereditary motor, type 7A;C4310694:Congenital myasthenic syndrome 20

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.060

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.39

CADD

Benign

DANN

Benign

0.70

DEOGEN2

Benign

0.11

T;T

Eigen

Benign

-0.38

Eigen_PC

Benign

-0.14

FATHMM_MKL

Uncertain

0.92

LIST_S2

Uncertain

0.89

.;D

MetaRNN

Benign

0.0027

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.47

N;N

MutationTaster

Benign

0.0013

P;P;P

PrimateAI

Benign

0.33

PROVEAN

Benign

-0.44

N;N

REVEL

Uncertain

0.32

Sift

Benign

0.44

T;T

Sift4G

Benign

0.76

T;T

Polyphen

0.015

B;B

Vest4

0.045

MPC

0.70

ClinPred

0.012

GERP RS

3.8

Varity_R

0.10

gMVP

0.65

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over