Variant 6-31870936-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_025257.3(SLC44A4):c.813C>T(p.Tyr271Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 1,612,452 control chromosomes in the GnomAD database, including 138,800 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.42 ( 13732 hom., cov: 31)

Exomes 𝑓: 0.41 ( 125068 hom. )

Consequence

SLC44A4
NM_025257.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.18

Variant links:

Genes affected

SLC44A4 (HGNC:13941): (solute carrier family 44 member 4) The protein encoded by this gene may be a sodium-dependent transmembrane transport protein involved in the uptake of choline by cholinergic neurons. Defects in this gene can cause sialidosis, a lysosomal storage disease. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]

SLC44A4 links:

SLC44A4 (HGNC:):

SLC44A4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant 6-31870936-G-A is Benign according to our data. Variant chr6-31870936-G-A is described in ClinVar as [Benign]. Clinvar id is 1279733.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.18 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC44A4	NM_025257.3 linkuse as main transcript	c.813C>T	p.Tyr271Tyr	synonymous_variant	10/21	ENST00000229729.11	NP_079533.2	Q53GD3-1A0A140VJH4
SLC44A4	NM_001178044.2 linkuse as main transcript	c.687C>T	p.Tyr229Tyr	synonymous_variant	9/20		NP_001171515.1	Q53GD3-4
SLC44A4	NM_001178045.2 linkuse as main transcript	c.585C>T	p.Tyr195Tyr	synonymous_variant	10/21		NP_001171516.1	Q53GD3-3A0A1U9X8K7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC44A4	ENST00000229729.11 linkuse as main transcript	c.813C>T	p.Tyr271Tyr	synonymous_variant	10/21	1	NM_025257.3	ENSP00000229729.6		Q53GD3-1
SLC44A4	ENST00000414427.1 linkuse as main transcript	c.686+378C>T		intron_variant		5		ENSP00000398901.1		H0Y5I3

Frequencies

GnomAD3 genomes

AF:

0.421

AC:

63940

AN:

151796

Hom.:

13729

Cov.:

show subpopulations

Gnomad AFR

AF:

0.423

Gnomad AMI

AF:

0.411

Gnomad AMR

AF:

0.457

Gnomad ASJ

AF:

0.647

Gnomad EAS

AF:

0.433

Gnomad SAS

AF:

0.405

Gnomad FIN

AF:

0.344

Gnomad MID

AF:

0.582

Gnomad NFE

AF:

0.411

Gnomad OTH

AF:

0.453

GnomAD3 exomes

AF:

0.437

AC:

107556

AN:

245914

Hom.:

24388

AF XY:

0.438

AC XY:

58645

AN XY:

134016

show subpopulations

Gnomad AFR exome

AF:

0.421

Gnomad AMR exome

AF:

0.491

Gnomad ASJ exome

AF:

0.653

Gnomad EAS exome

AF:

0.440

Gnomad SAS exome

AF:

0.409

Gnomad FIN exome

AF:

0.352

Gnomad NFE exome

AF:

0.427

Gnomad OTH exome

AF:

0.448

GnomAD4 exome

AF:

0.408

AC:

595644

AN:

1460536

Hom.:

125068

Cov.:

AF XY:

0.411

AC XY:

298745

AN XY:

726588

show subpopulations

Gnomad4 AFR exome

AF:

0.427

Gnomad4 AMR exome

AF:

0.489

Gnomad4 ASJ exome

AF:

0.646

Gnomad4 EAS exome

AF:

0.515

Gnomad4 SAS exome

AF:

0.414

Gnomad4 FIN exome

AF:

0.341

Gnomad4 NFE exome

AF:

0.396

Gnomad4 OTH exome

AF:

0.409

GnomAD4 genome

AF:

0.421

AC:

63978

AN:

151916

Hom.:

13732

Cov.:

AF XY:

0.421

AC XY:

31263

AN XY:

74242

show subpopulations

Gnomad4 AFR

AF:

0.423

Gnomad4 AMR

AF:

0.456

Gnomad4 ASJ

AF:

0.647

Gnomad4 EAS

AF:

0.434

Gnomad4 SAS

AF:

0.405

Gnomad4 FIN

AF:

0.344

Gnomad4 NFE

AF:

0.412

Gnomad4 OTH

AF:

0.450

Alfa

AF:

0.434

Hom.:

21529

Bravo

AF:

0.432

Asia WGS

AF:

0.389

AC:

1358

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -

Hearing loss, autosomal dominant 72

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

0.99

DANN

Benign

0.72

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