Genetic Variant SLC16A1:c.362-30_362-11delTATTTATTTATTTATTTATT (chr1-112918054-CAATAAATAAATAAATAAATA-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_003051.4(SLC16A1):c.362-30_362-11delTATTTATTTATTTATTTATT variant causes a intron change. The variant allele was found at a frequency of 0.00225 in 859,830 control chromosomes in the GnomAD database, including 59 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0019 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0023 ( 59 hom. )

Consequence

SLC16A1
NM_003051.4 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:2

Conservation

PhyloP100: 3.97

Variant links:

Genes affected

SLC16A1 (HGNC:10922): (solute carrier family 16 member 1) The protein encoded by this gene is a proton-linked monocarboxylate transporter that catalyzes the movement of many monocarboxylates, such as lactate and pyruvate, across the plasma membrane. Mutations in this gene are associated with erythrocyte lactate transporter defect. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Oct 2009]

SLC16A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 1-112918054-CAATAAATAAATAAATAAATA-C is Benign according to our data. Variant chr1-112918054-CAATAAATAAATAAATAAATA-C is described in ClinVar as [Likely_benign]. Clinvar id is 1629202.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00187 (271/144636) while in subpopulation NFE AF= 0.00209 (139/66424). AF 95% confidence interval is 0.00181. There are 0 homozygotes in gnomad4. There are 121 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High Homozygotes in GnomAdExome4 at 59 SD gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SLC16A1	NM_003051.4 link	c.362-30_362-11delTATTTATTTATTTATTTATT	intron_variant	Intron 3 of 4	ENST00000369626.8	NP_003042.3	P53985-1A0A024R0H1
SLC16A1	NM_001166496.2 link	c.362-30_362-11delTATTTATTTATTTATTTATT	intron_variant	Intron 3 of 4		NP_001159968.1	P53985-1A0A024R0H1B4DKS0
SLC16A1	XM_047428789.1 link	c.362-30_362-11delTATTTATTTATTTATTTATT	intron_variant	Intron 3 of 4		XP_047284745.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC16A1	ENST00000369626.8 link	c.362-30_362-11delTATTTATTTATTTATTTATT		intron_variant	Intron 3 of 4	1	NM_003051.4	ENSP00000358640.4		P53985-1

Frequencies

GnomAD3 genomes

AF:

0.00185

AC:

268

AN:

144564

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00181

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000895

Gnomad ASJ

AF:

0.00582

Gnomad EAS

AF:

0.000200

Gnomad SAS

AF:

0.00154

Gnomad FIN

AF:

0.00193

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00209

Gnomad OTH

AF:

0.000506

GnomAD3 exomes

AF:

0.00183

AC:

111

AN:

60732

Hom.:

AF XY:

0.00179

AC XY:

AN XY:

35678

show subpopulations

Gnomad AFR exome

AF:

0.000604

Gnomad AMR exome

AF:

0.00227

Gnomad ASJ exome

AF:

0.00400

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00243

Gnomad FIN exome

AF:

0.000965

Gnomad NFE exome

AF:

0.00163

Gnomad OTH exome

AF:

0.00636

GnomAD4 exome

AF:

0.00232

AC:

1662

AN:

715194

Hom.:

AF XY:

0.00235

AC XY:

849

AN XY:

362038

show subpopulations

Gnomad4 AFR exome

AF:

0.00328

Gnomad4 AMR exome

AF:

0.00170

Gnomad4 ASJ exome

AF:

0.00678

Gnomad4 EAS exome

AF:

0.000206

Gnomad4 SAS exome

AF:

0.00383

Gnomad4 FIN exome

AF:

0.00310

Gnomad4 NFE exome

AF:

0.00218

Gnomad4 OTH exome

AF:

0.00267

GnomAD4 genome

AF:

0.00187

AC:

271

AN:

144636

Hom.:

Cov.:

AF XY:

0.00172

AC XY:

121

AN XY:

70218

show subpopulations

Gnomad4 AFR

AF:

0.00188

Gnomad4 AMR

AF:

0.000894

Gnomad4 ASJ

AF:

0.00582

Gnomad4 EAS

AF:

0.000201

Gnomad4 SAS

AF:

0.00155

Gnomad4 FIN

AF:

0.00193

Gnomad4 NFE

AF:

0.00209

Gnomad4 OTH

AF:

0.000500

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jan 27, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

SLC16A1-related disorder

Benign:1

May 11, 2022

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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.

1-112918054-CAATAAATAAATAAATAAATAAATAAATAAATA-CAATAAATAAATA

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