Variant 1-112918054-CAATAAATAAATAAATAAATAAATA-CAATAAATAAATAAATAAATAAATAAATA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2

The NM_003051.4(SLC16A1):c.362-11_362-10insTATT variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.0064 ( 5 hom., cov: 0)

Exomes 𝑓: 0.0026 ( 2 hom. )

Consequence

SLC16A1
NM_003051.4 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:2

Conservation

PhyloP100: -0.497

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant 1-112918054-C-CAATA is Benign according to our data. Variant chr1-112918054-C-CAATA is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 1336772.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Uncertain_significance=1}.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00643 (930/144614) while in subpopulation AFR AF= 0.0102 (395/38742). AF 95% confidence interval is 0.00937. There are 5 homozygotes in gnomad4. There are 476 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 5 SD gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
SLC16A1	NM_003051.4 linkuse as main transcript	c.362-11_362-10insTATT	splice_polypyrimidine_tract_variant, intron_variant	ENST00000369626.8	NP_003042.3
SLC16A1	NM_001166496.2 linkuse as main transcript	c.362-11_362-10insTATT	splice_polypyrimidine_tract_variant, intron_variant		NP_001159968.1
SLC16A1	XM_047428789.1 linkuse as main transcript	c.362-11_362-10insTATT	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 linkuse as main transcript	c.362-11_362-10insTATT		splice_polypyrimidine_tract_variant, intron_variant		1	NM_003051.4	ENSP00000358640	P1	P53985-1

Frequencies

GnomAD3 genomes

AF:

0.00644

AC:

931

AN:

144542

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0102

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00524

Gnomad ASJ

AF:

0.000582

Gnomad EAS

AF:

0.00440

Gnomad SAS

AF:

0.00132

Gnomad FIN

AF:

0.0174

Gnomad MID

AF:

0.00649

Gnomad NFE

AF:

0.00393

Gnomad OTH

AF:

0.00708

GnomAD3 exomes

AF:

0.000856

AC:

AN:

60732

Hom.:

AF XY:

0.000813

AC XY:

AN XY:

35678

show subpopulations

Gnomad AFR exome

AF:

0.000302

Gnomad AMR exome

AF:

0.000227

Gnomad ASJ exome

AF:

0.000308

Gnomad EAS exome

AF:

0.00114

Gnomad SAS exome

AF:

0.000970

Gnomad FIN exome

AF:

0.00231

Gnomad NFE exome

AF:

0.000770

Gnomad OTH exome

AF:

0.000795

GnomAD4 exome

AF:

0.00256

AC:

1830

AN:

714864

Hom.:

Cov.:

AF XY:

0.00250

AC XY:

904

AN XY:

361898

show subpopulations

Gnomad4 AFR exome

AF:

0.00779

Gnomad4 AMR exome

AF:

0.00201

Gnomad4 ASJ exome

AF:

0.000909

Gnomad4 EAS exome

AF:

0.00144

Gnomad4 SAS exome

AF:

0.00148

Gnomad4 FIN exome

AF:

0.00531

Gnomad4 NFE exome

AF:

0.00247

Gnomad4 OTH exome

AF:

0.00273

GnomAD4 genome

AF:

0.00643

AC:

930

AN:

144614

Hom.:

Cov.:

AF XY:

0.00678

AC XY:

476

AN XY:

70210

show subpopulations

Gnomad4 AFR

AF:

0.0102

Gnomad4 AMR

AF:

0.00523

Gnomad4 ASJ

AF:

0.000582

Gnomad4 EAS

AF:

0.00421

Gnomad4 SAS

AF:

0.00133

Gnomad4 FIN

AF:

0.0174

Gnomad4 NFE

AF:

0.00393

Gnomad4 OTH

AF:

0.00700

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1Benign:2

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Nov 01, 2022	SLC16A1: BS2 -
Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Nov 11, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over