1-112918054-CAATAAATAAATAAATAAATAAATAAATAAATA-CAATAAATAAATAAATA

Variant names:

• chr1-112918054-CAATAAATAAATAAATA-C
• rs149491709
• NM_003051.4:c.362-26_362-11delTATTTATTTATTTATT

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The NM_003051.4(SLC16A1):​c.362-26_362-11delTATTTATTTATTTATT variant causes a intron change. The variant allele was found at a frequency of 0.0139 in 859,730 control chromosomes in the GnomAD database, including 831 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.014 (32 hom., cov: 0)
  • Exomes 𝑓: 0.014 (799 hom.)
• Consequence: SLC16A1 NM_003051.4 intron
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 3.97
• Publications: 1 publications found

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-AS1 (HGNC:49445): (SLC16A1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -16 ACMG points.

• BP6: Variant 1-112918054-CAATAAATAAATAAATA-C is Benign according to our data. Variant chr1-112918054-CAATAAATAAATAAATA-C is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 1570647.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A1	NM_003051.4	c.362-26_362-11delTATTTATTTATTTATT		intron_variant	Intron 3 of 4	ENST00000369626.8	NP_003042.3
SLC16A1	NM_001166496.2	c.362-26_362-11delTATTTATTTATTTATT		intron_variant	Intron 3 of 4		NP_001159968.1
SLC16A1	XM_047428789.1	c.362-26_362-11delTATTTATTTATTTATT		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	c.362-26_362-11delTATTTATTTATTTATT		intron_variant	Intron 3 of 4	1	NM_003051.4	ENSP00000358640.4

Frequencies

GnomAD3 genomes AF: 0.0136 AC: 1963 AN: 144554 Hom.: 30 Cov.: 0

Gnomad AFR AF: 0.0167

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0145

Gnomad ASJ AF: 0.00116

Gnomad EAS AF: 0.0581

Gnomad SAS AF: 0.0324

Gnomad FIN AF: 0.00614

Gnomad MID AF: 0.00325

Gnomad NFE AF: 0.00888

Gnomad OTH AF: 0.0106

GnomAD2 exomes AF: 0.0162 AC: 985 AN: 60732 AF XY: 0.0172

Gnomad AFR exome AF: 0.00483

Gnomad AMR exome AF: 0.0193

Gnomad ASJ exome AF: 0.00462

Gnomad EAS exome AF: 0.130

Gnomad FIN exome AF: 0.00424

Gnomad NFE exome AF: 0.00447

Gnomad OTH exome AF: 0.00874

GnomAD4 exome AF: 0.0139 AC: 9965 AN: 715104 Hom.: 799 AF XY: 0.0148 AC XY: 5341 AN XY: 361992

African (AFR) AF: 0.0204 AC: 299 AN: 14648

American (AMR) AF: 0.0235 AC: 304 AN: 12934

Ashkenazi Jewish (ASJ) AF: 0.00322 AC: 46 AN: 14302

East Asian (EAS) AF: 0.0824 AC: 2003 AN: 24296

South Asian (SAS) AF: 0.0715 AC: 1641 AN: 22964

European-Finnish (FIN) AF: 0.00854 AC: 179 AN: 20954

Middle Eastern (MID) AF: 0.00768 AC: 17 AN: 2214

European-Non Finnish (NFE) AF: 0.00881 AC: 5040 AN: 572034

Other (OTH) AF: 0.0142 AC: 436 AN: 30758

GnomAD4 genome AF: 0.0136 AC: 1966 AN: 144626 Hom.: 32 Cov.: 0 AF XY: 0.0147 AC XY: 1034 AN XY: 70212

African (AFR) AF: 0.0167 AC: 646 AN: 38746

American (AMR) AF: 0.0149 AC: 216 AN: 14532

Ashkenazi Jewish (ASJ) AF: 0.00116 AC: 4 AN: 3438

East Asian (EAS) AF: 0.0584 AC: 291 AN: 4982

South Asian (SAS) AF: 0.0319 AC: 144 AN: 4516

European-Finnish (FIN) AF: 0.00614 AC: 54 AN: 8800

Middle Eastern (MID) AF: 0.00352 AC: 1 AN: 284

European-Non Finnish (NFE) AF: 0.00888 AC: 590 AN: 66424

Other (OTH) AF: 0.0100 AC: 20 AN: 2000

Alfa AF: 0.0204 Hom.: 967

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Metabolic myopathy due to lactate transporter defect;C1864902:Exercise-induced hyperinsulinism;C4015186:Ketoacidosis due to monocarboxylate transporter-1 deficiency Benign:1

Jan 21, 2022

Fulgent Genetics, Fulgent Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs149491709; hg19: chr1-113460676;