Variant chr17-7041898-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BS1BS2

The NM_001370549.1(SLC16A11):c.1125G>A(p.Arg375=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00143 in 1,613,878 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0076 ( 13 hom., cov: 32)

Exomes 𝑓: 0.00078 ( 16 hom. )

Consequence

SLC16A11
NM_001370549.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.585

Variant links:

Genes affected

SLC16A11 (HGNC:23093): (solute carrier family 16 member 11) Enables pyruvate transmembrane transporter activity. Involved in lipid metabolic process. Located in endoplasmic reticulum membrane and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC16A11 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP7

Synonymous conserved (PhyloP=0.585 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0076 (1156/152180) while in subpopulation AFR AF= 0.0259 (1077/41510). AF 95% confidence interval is 0.0247. There are 13 homozygotes in gnomad4. There are 539 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 13 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
SLC16A11	NM_001370549.1 linkuse as main transcript	c.1125G>A	p.Arg375=	synonymous_variant	5/5	ENST00000574600.3	NP_001357478.1
SLC16A11	NM_153357.3 linkuse as main transcript	c.1125G>A	p.Arg375=	synonymous_variant	4/4		NP_699188.2
SLC16A11	NM_001370553.1 linkuse as main transcript	c.*33G>A		3_prime_UTR_variant	4/4		NP_001357482.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
SLC16A11	ENST00000574600.3 linkuse as main transcript	c.1125G>A	p.Arg375=	synonymous_variant	5/5	3	NM_001370549.1	ENSP00000460927	P1
SLC16A11	ENST00000573338.1 linkuse as main transcript	n.688G>A		non_coding_transcript_exon_variant	2/2	1
SLC16A11	ENST00000662352.3 linkuse as main transcript	c.1125G>A	p.Arg375=	synonymous_variant	4/4			ENSP00000499634	P1
SLC16A11	ENST00000673828.2 linkuse as main transcript	c.*33G>A		3_prime_UTR_variant	4/4			ENSP00000501313

Frequencies

GnomAD3 genomes

AF:

0.00756

AC:

1149

AN:

152062

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0258

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00367

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0000735

Gnomad OTH

AF:

0.00766

GnomAD3 exomes

AF:

0.00196

AC:

486

AN:

247912

Hom.:

AF XY:

0.00149

AC XY:

201

AN XY:

134938

show subpopulations

Gnomad AFR exome

AF:

0.0271

Gnomad AMR exome

AF:

0.00148

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000981

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000716

Gnomad OTH exome

AF:

0.00116

GnomAD4 exome

AF:

0.000783

AC:

1144

AN:

1461698

Hom.:

Cov.:

AF XY:

0.000710

AC XY:

516

AN XY:

727156

show subpopulations

Gnomad4 AFR exome

AF:

0.0263

Gnomad4 AMR exome

AF:

0.00172

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000812

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000459

Gnomad4 OTH exome

AF:

0.00200

GnomAD4 genome

AF:

0.00760

AC:

1156

AN:

152180

Hom.:

Cov.:

AF XY:

0.00724

AC XY:

539

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.0259

Gnomad4 AMR

AF:

0.00366

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000736

Gnomad4 OTH

AF:

0.00758

Alfa

AF:

0.00286

Hom.:

Bravo

AF:

0.00876

Asia WGS

AF:

0.00173

AC:

AN:

3478

EpiCase

AF:

0.000164

EpiControl

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

7.3

DANN

Benign

0.82

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over