Variant chr21-42539566-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001320537.2(SLC37A1):c.405C>T(p.Leu135=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0115 in 1,613,944 control chromosomes in the GnomAD database, including 150 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. L135L) has been classified as Benign.

Frequency

Genomes: 𝑓 0.0097 ( 22 hom., cov: 33)

Exomes 𝑓: 0.012 ( 128 hom. )

Consequence

SLC37A1
NM_001320537.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.863

Variant links:

Genes affected

SLC37A1 (HGNC:11024): (solute carrier family 37 member 1) The protein encoded by this gene localizes to the endoplasmic reticulum (ER) membrane. This protein translocates glucose-6-phosphate from the cytoplasm into the lumen of the ER for hydrolysis into glucose by another ER membrane protein. This gene is a member of the solute carrier 37 gene family. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

SLC37A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP6

Variant 21-42539566-C-T is Benign according to our data. Variant chr21-42539566-C-T is described in ClinVar as [Benign]. Clinvar id is 777310.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.863 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 22 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC37A1	NM_001320537.2 linkuse as main transcript	c.405C>T	p.Leu135=	synonymous_variant	6/20	ENST00000352133.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC37A1	ENST00000352133.3 linkuse as main transcript	c.405C>T	p.Leu135=	synonymous_variant	6/20	1	NM_001320537.2	P1
SLC37A1	ENST00000398341.7 linkuse as main transcript	c.405C>T	p.Leu135=	synonymous_variant	7/21	1		P1

Frequencies

GnomAD3 genomes

AF:

0.00970

AC:

1477

AN:

152222

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00236

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.00451

Gnomad ASJ

AF:

0.00634

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00498

Gnomad FIN

AF:

0.0227

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0131

Gnomad OTH

AF:

0.00621

GnomAD3 exomes

AF:

0.00959

AC:

2408

AN:

251096

Hom.:

AF XY:

0.00998

AC XY:

1354

AN XY:

135700

show subpopulations

Gnomad AFR exome

AF:

0.00209

Gnomad AMR exome

AF:

0.00261

Gnomad ASJ exome

AF:

0.00586

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00729

Gnomad FIN exome

AF:

0.0217

Gnomad NFE exome

AF:

0.0131

Gnomad OTH exome

AF:

0.00767

GnomAD4 exome

AF:

0.0117

AC:

17128

AN:

1461604

Hom.:

128

Cov.:

AF XY:

0.0117

AC XY:

8498

AN XY:

727090

show subpopulations

Gnomad4 AFR exome

AF:

0.00131

Gnomad4 AMR exome

AF:

0.00338

Gnomad4 ASJ exome

AF:

0.00586

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00709

Gnomad4 FIN exome

AF:

0.0212

Gnomad4 NFE exome

AF:

0.0130

Gnomad4 OTH exome

AF:

0.00949

GnomAD4 genome

AF:

0.00969

AC:

1476

AN:

152340

Hom.:

Cov.:

AF XY:

0.00961

AC XY:

716

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.00236

Gnomad4 AMR

AF:

0.00451

Gnomad4 ASJ

AF:

0.00634

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00498

Gnomad4 FIN

AF:

0.0227

Gnomad4 NFE

AF:

0.0131

Gnomad4 OTH

AF:

0.00567

Alfa

AF:

0.00629

Hom.:

Bravo

AF:

0.00884

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jul 20, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

6.2

DANN

Benign

0.64

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