1-112918054-CAATAAATAAATAAATAAATAAATA-CAATA

Position:

• chr1-112918054-CAATAAATAAATAAATAAATAAATA-CAATA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

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
• Clinical Significance: Likely benign criteria provided, single submitter B:2
• Conservation: PhyloP100: 3.97

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 (HGNC:):

ACMG classification

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	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC16A1	NM_003051.4	c.362-30_362-11delTATTTATTTATTTATTTATT		intron_variant		ENST00000369626.8	NP_003042.3
SLC16A1	NM_001166496.2	c.362-30_362-11delTATTTATTTATTTATTTATT		intron_variant			NP_001159968.1
SLC16A1	XM_047428789.1	c.362-30_362-11delTATTTATTTATTTATTTATT		intron_variant			XP_047284745.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC16A1	ENST00000369626.8	c.362-30_362-11delTATTTATTTATTTATTTATT		intron_variant		1	NM_003051.4	ENSP00000358640.4

Frequencies

GnomAD3 genomes AF: 0.00185 AC: 268 AN: 144564 Hom.: 0 Cov.: 0

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.: 15 AF XY: 0.00179 AC XY: 64 AN XY: 35678

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.: 59 AF XY: 0.00235 AC XY: 849 AN XY: 362038

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.: 0 Cov.: 0 AF XY: 0.00172 AC XY: 121 AN XY: 70218

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

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 22, 2024

- -

SLC16A1-related disorder Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

May 11, 2022

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

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs149491709; hg19: chr1-113460676;