1-112918054-CAATAAATAAATAAATAAATAAATA-CAATAAATAAATAAATAAATAAATAAATAAATA

Position:

• chr1-112918054-CAATAAATAAATAAATAAATAAATA-CAATAAATAAATAAATAAATAAATAAATAAATA

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_003051.4(SLC16A1):​c.362-18_362-11dupTATTTATT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00013 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000080 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC16A1 NM_003051.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.497

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 Likely_benign. Variant got -2 ACMG points.

• BP6: Variant 1-112918054-C-CAATAAATA is Benign according to our data. Variant chr1-112918054-C-CAATAAATA is described in ClinVar as [Likely_benign]. Clinvar id is 1896003.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.000131 AC: 19 AN: 144568 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000285

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000689

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: 0.000105

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000797 AC: 57 AN: 715202 Hom.: 0 Cov.: 0 AF XY: 0.0000911 AC XY: 33 AN XY: 362046

Gnomad4 AFR exome AF: 0.000341

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000412

Gnomad4 SAS exome AF: 0.000131

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000787

Gnomad4 OTH exome AF: 0.0000325

GnomAD4 genome AF: 0.000131 AC: 19 AN: 144640 Hom.: 0 Cov.: 0 AF XY: 0.000142 AC XY: 10 AN XY: 70222

Gnomad4 AFR AF: 0.000284

Gnomad4 AMR AF: 0.0000688

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000105

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

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

Jun 09, 2023

- -

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;