1-112918054-CAATAAATAAATAAATAAATAAATAAATAAATA-CAATAAATAAATAAATAAATAAATA

Variant names:

• chr1-112918054-CAATAAATA-C
• rs149491709
• NM_003051.4:c.362-18_362-11delTATTTATT

Variant summary

Our verdict is Benign. The variant received -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
• 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 -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003051.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A1	NM_003051.4	MANE Select	c.362-18_362-11delTATTTATT		intron	N/A	NP_003042.3
	SLC16A1	NM_001166496.2		c.362-18_362-11delTATTTATT		intron	N/A	NP_001159968.1	P53985-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A1	ENST00000369626.8	TSL:1 MANE Select	c.362-18_362-11delTATTTATT		intron	N/A	ENSP00000358640.4	P53985-1
	SLC16A1	ENST00000429288.2	TSL:3	c.362-18_362-11delTATTTATT		intron	N/A	ENSP00000397106.2	P53985-1
	SLC16A1	ENST00000443580.6	TSL:3	c.362-18_362-11delTATTTATT		intron	N/A	ENSP00000399104.2	P53985-1

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

GnomAD2 exomes AF: 0.0576 AC: 3496 AN: 60732 AF XY: 0.0596

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 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

African (AFR) AF: 0.151 AC: 2157 AN: 14312

American (AMR) AF: 0.144 AC: 1810 AN: 12612

Ashkenazi Jewish (ASJ) AF: 0.0976 AC: 1362 AN: 13948

East Asian (EAS) AF: 0.0641 AC: 1519 AN: 23704

South Asian (SAS) AF: 0.0848 AC: 1911 AN: 22544

European-Finnish (FIN) AF: 0.132 AC: 2695 AN: 20476

Middle Eastern (MID) AF: 0.134 AC: 286 AN: 2138

European-Non Finnish (NFE) AF: 0.144 AC: 80388 AN: 560122

Other (OTH) AF: 0.138 AC: 4146 AN: 30028

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

African (AFR) AF: 0.171 AC: 6608 AN: 38642

American (AMR) AF: 0.222 AC: 3212 AN: 14494

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 452 AN: 3430

East Asian (EAS) AF: 0.0664 AC: 330 AN: 4972

South Asian (SAS) AF: 0.116 AC: 524 AN: 4504

European-Finnish (FIN) AF: 0.213 AC: 1866 AN: 8774

Middle Eastern (MID) AF: 0.144 AC: 41 AN: 284

European-Non Finnish (NFE) AF: 0.182 AC: 12030 AN: 66234

Other (OTH) AF: 0.181 AC: 360 AN: 1990

Alfa AF: 0.160 Hom.: 967

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

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;