1-112912805-T-TA

Variant names:

• chr1-112912805-T-TA
• rs886045060
• NM_003051.4:c.*1085dupT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_003051.4(SLC16A1):​c.*1085dupT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★★).

• Frequency:
  • Genomes: 𝑓 0.0048 (1 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC16A1 NM_003051.4 3_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:2
• Conservation: PhyloP100: -0.312

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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A1	NM_003051.4	c.*1085dupT		3_prime_UTR_variant	Exon 5 of 5	ENST00000369626.8	NP_003042.3
SLC16A1	NM_001166496.2	c.*1085dupT		3_prime_UTR_variant	Exon 5 of 5		NP_001159968.1
SLC16A1	XM_047428789.1	c.*1085dupT		3_prime_UTR_variant	Exon 5 of 5		XP_047284745.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC16A1	ENST00000369626	c.*1085dupT		3_prime_UTR_variant	Exon 5 of 5	1	NM_003051.4	ENSP00000358640.4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 645 AN: 136222 Hom.: 1 Cov.: 32 FAILED QC

Gnomad AFR AF: 0.00656

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00519

Gnomad ASJ AF: 0.00187

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.00804

Gnomad FIN AF: 0.00694

Gnomad MID AF: 0.00690

Gnomad NFE AF: 0.00349

Gnomad OTH AF: 0.00165

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00476 AC: 649 AN: 136254 Hom.: 1 Cov.: 32 AF XY: 0.00524 AC XY: 345 AN XY: 65888

Gnomad4 AFR AF: 0.00668

Gnomad4 AMR AF: 0.00526

Gnomad4 ASJ AF: 0.00187

Gnomad4 EAS AF: 0.00229

Gnomad4 SAS AF: 0.00808

Gnomad4 FIN AF: 0.00694

Gnomad4 NFE AF: 0.00349

Gnomad4 OTH AF: 0.00164

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Uncertain:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Hyperinsulinism, Dominant Uncertain:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs886045060; hg19: chr1-113455427;