1-112918054-CAATAAATA-C

Position:

• chr1-112918054-CAATAAATA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_003051.4(SLC16A1):​c.362-18_362-11delTATTTATT variant causes a intron change. The variant allele was found at a frequency of 0.144 in 844,110 control chromosomes in the GnomAD database, including 11,538 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.18 (2408 hom., cov: 0)
  • Exomes 𝑓: 0.14 (9130 hom.)
• Consequence: SLC16A1 NM_003051.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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-CAATAAATA-C is Benign according to our data. Variant chr1-112918054-CAATAAATA-C is described in ClinVar as [Benign]. Clinvar id is 1601388.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC16A1	NM_003051.4	c.362-18_362-11delTATTTATT		intron_variant		ENST00000369626.8	NP_003042.3
SLC16A1	NM_001166496.2	c.362-18_362-11delTATTTATT		intron_variant			NP_001159968.1
SLC16A1	XM_047428789.1	c.362-18_362-11delTATTTATT		intron_variant			XP_047284745.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC16A1	ENST00000369626.8	c.362-18_362-11delTATTTATT		intron_variant		1	NM_003051.4	ENSP00000358640.4

Frequencies

GnomAD3 genomes AF: 0.177 AC: 25566 AN: 144154 Hom.: 2403 Cov.: 0

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0664

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.182

GnomAD3 exomes AF: 0.0576 AC: 3496 AN: 60732 Hom.: 305 AF XY: 0.0596 AC XY: 2126 AN XY: 35678

Gnomad AFR exome AF: 0.0124

Gnomad AMR exome AF: 0.0453

Gnomad ASJ exome AF: 0.0801

Gnomad EAS exome AF: 0.0103

Gnomad SAS exome AF: 0.0746

Gnomad FIN exome AF: 0.0710

Gnomad NFE exome AF: 0.0586

Gnomad OTH exome AF: 0.0668

GnomAD4 exome AF: 0.138 AC: 96274 AN: 699884 Hom.: 9130 AF XY: 0.138 AC XY: 48949 AN XY: 353956

Gnomad4 AFR exome AF: 0.151

Gnomad4 AMR exome AF: 0.144

Gnomad4 ASJ exome AF: 0.0976

Gnomad4 EAS exome AF: 0.0641

Gnomad4 SAS exome AF: 0.0848

Gnomad4 FIN exome AF: 0.132

Gnomad4 NFE exome AF: 0.144

Gnomad4 OTH exome AF: 0.138

GnomAD4 genome AF: 0.177 AC: 25583 AN: 144226 Hom.: 2408 Cov.: 0 AF XY: 0.177 AC XY: 12397 AN XY: 70020

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0664

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.181

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

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;