rs149491709

Positions:

• chr1-112918054-CAATAAATAAATAAATAAATAAATA-C
• chr1-112918054-CAATAAATAAATAAATAAATAAATA-CAATA
• chr1-112918054-CAATAAATAAATAAATAAATAAATA-CAATAAATA
• chr1-112918054-CAATAAATAAATAAATAAATAAATA-CAATAAATAAATA
• chr1-112918054-CAATAAATAAATAAATAAATAAATA-CAATAAATAAATAAATA
• chr1-112918054-CAATAAATAAATAAATAAATAAATA-CAATAAATAAATAAATAAATA
• chr1-112918054-CAATAAATAAATAAATAAATAAATA-CAATAAATAAATAAATAAATAAATAAATA
• chr1-112918054-CAATAAATAAATAAATAAATAAATA-CAATAAATAAATAAATAAATAAATAAATAAATA

Variant summary

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

The NM_003051.4(SLC16A1):​c.362-34_362-11del variant causes a splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.000533 in 859,840 control chromosomes in the GnomAD database, including 24 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0017 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00030 (24 hom.)
• Consequence: SLC16A1 NM_003051.4 splice_polypyrimidine_tract, 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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-112918054-CAATAAATAAATAAATAAATAAATA-C is Benign according to our data. Variant chr1-112918054-CAATAAATAAATAAATAAATAAATA-C is described in ClinVar as [Benign]. Clinvar id is 1672528.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00169 (245/144640) while in subpopulation AFR AF= 0.00588 (228/38748). AF 95% confidence interval is 0.00526. There are 0 homozygotes in gnomad4. There are 103 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAdExome4 at 24 SD gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC16A1	NM_003051.4	c.362-34_362-11del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000369626.8	NP_003042.3
SLC16A1	NM_001166496.2	c.362-34_362-11del		splice_polypyrimidine_tract_variant, intron_variant			NP_001159968.1
SLC16A1	XM_047428789.1	c.362-34_362-11del		splice_polypyrimidine_tract_variant, intron_variant			XP_047284745.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC16A1	ENST00000369626.8	c.362-34_362-11del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_003051.4	ENSP00000358640	P1

Frequencies

GnomAD3 genomes AF: 0.00169 AC: 245 AN: 144568 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00590

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000758

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000753

Gnomad OTH AF: 0.000506

GnomAD4 exome AF: 0.000298 AC: 213 AN: 715200 Hom.: 24 AF XY: 0.000262 AC XY: 95 AN XY: 362046

Gnomad4 AFR exome AF: 0.00996

Gnomad4 AMR exome AF: 0.000695

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000477

Gnomad4 NFE exome AF: 0.0000559

Gnomad4 OTH exome AF: 0.000715

GnomAD4 genome AF: 0.00169 AC: 245 AN: 144640 Hom.: 0 Cov.: 0 AF XY: 0.00147 AC XY: 103 AN XY: 70222

Gnomad4 AFR AF: 0.00588

Gnomad4 AMR AF: 0.000757

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000753

Gnomad4 OTH AF: 0.000500

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

Jan 10, 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;