Genetic Variant SLC16A1:c.362-14_362-11delTATT (chr1-112918054-CAATA-C) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_003051.4(SLC16A1):c.362-14_362-11delTATT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 855,896 control chromosomes in the GnomAD database, including 143,238 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.62 ( 27489 hom., cov: 0)

Exomes 𝑓: 0.52 ( 115749 hom. )

Consequence

SLC16A1
NM_003051.4 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.375

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 -16 ACMG points.

BP6

Variant 1-112918054-CAATA-C is Benign according to our data. Variant chr1-112918054-CAATA-C is described in ClinVar as [Likely_benign]. Clinvar id is 291868.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-112918054-CAATA-C is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SLC16A1	NM_003051.4 link	c.362-14_362-11delTATT	intron_variant	Intron 3 of 4	ENST00000369626.8	NP_003042.3	P53985-1A0A024R0H1
SLC16A1	NM_001166496.2 link	c.362-14_362-11delTATT	intron_variant	Intron 3 of 4		NP_001159968.1	P53985-1A0A024R0H1B4DKS0
SLC16A1	XM_047428789.1 link	c.362-14_362-11delTATT	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.362-14_362-11delTATT		intron_variant	Intron 3 of 4	1	NM_003051.4	ENSP00000358640.4		P53985-1

Frequencies

GnomAD3 genomes

AF:

0.616

AC:

88865

AN:

144204

Hom.:

27482

Cov.:

show subpopulations

Gnomad AFR

AF:

0.587

Gnomad AMI

AF:

0.777

Gnomad AMR

AF:

0.629

Gnomad ASJ

AF:

0.713

Gnomad EAS

AF:

0.640

Gnomad SAS

AF:

0.724

Gnomad FIN

AF:

0.553

Gnomad MID

AF:

0.682

Gnomad NFE

AF:

0.622

Gnomad OTH

AF:

0.600

GnomAD3 exomes

AF:

0.322

AC:

19552

AN:

60732

Hom.:

6587

AF XY:

0.332

AC XY:

11832

AN XY:

35678

show subpopulations

Gnomad AFR exome

AF:

0.0679

Gnomad AMR exome

AF:

0.241

Gnomad ASJ exome

AF:

0.613

Gnomad EAS exome

AF:

0.318

Gnomad SAS exome

AF:

0.515

Gnomad FIN exome

AF:

0.347

Gnomad NFE exome

AF:

0.275

Gnomad OTH exome

AF:

0.362

GnomAD4 exome

AF:

0.517

AC:

368245

AN:

711622

Hom.:

115749

AF XY:

0.520

AC XY:

187468

AN XY:

360180

show subpopulations

Gnomad4 AFR exome

AF:

0.449

Gnomad4 AMR exome

AF:

0.452

Gnomad4 ASJ exome

AF:

0.654

Gnomad4 EAS exome

AF:

0.627

Gnomad4 SAS exome

AF:

0.544

Gnomad4 FIN exome

AF:

0.488

Gnomad4 NFE exome

AF:

0.511

Gnomad4 OTH exome

AF:

0.548

GnomAD4 genome

AF:

0.616

AC:

88894

AN:

144274

Hom.:

27489

Cov.:

AF XY:

0.616

AC XY:

43142

AN XY:

70026

show subpopulations

Gnomad4 AFR

AF:

0.587

Gnomad4 AMR

AF:

0.629

Gnomad4 ASJ

AF:

0.713

Gnomad4 EAS

AF:

0.640

Gnomad4 SAS

AF:

0.724

Gnomad4 FIN

AF:

0.553

Gnomad4 NFE

AF:

0.622

Gnomad4 OTH

AF:

0.603

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 09, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hyperinsulinism, Dominant

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

SLC16A1-related disorder

Benign:1

Jun 18, 2021

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as 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

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.

1-112918054-CAATAAATAAATAAATAAATAAATAAATAAATA-CAATAAATAAATAAATAAATAAATAAATA

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