Genetic Variant SLC16A1:c.362-14_362-11dupTATT (chr1-112918054-C-CAATA) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP6BS1BS2

The NM_003051.4(SLC16A1):c.362-14_362-11dupTATT variant causes a 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 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 was made for transcript

Our verdict: Benign. The variant received -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: {Uncertain_significance=1, Likely_benign=2}.

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 the male GnomAd4 subpopulation. Median coverage is 0. This position FAILED quality control check.

BS2

High Homozygotes in GnomAd4 at 5 SD gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SLC16A1	NM_003051.4 link	c.362-14_362-11dupTATT	intron_variant	Intron 3 of 4	ENST00000369626.8	NP_003042.3	P53985-1A0A024R0H1
SLC16A1	NM_001166496.2 link	c.362-14_362-11dupTATT	intron_variant	Intron 3 of 4		NP_001159968.1	P53985-1A0A024R0H1B4DKS0
SLC16A1	XM_047428789.1 link	c.362-14_362-11dupTATT	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 link	c.362-11_362-10insTATT		intron_variant	Intron 3 of 4	1	NM_003051.4	ENSP00000358640.4		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

GnomAD2 exomes

AF:

0.000856

AC:

AN:

60732

AF XY:

0.000813

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 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

AC:

114

AN:

14632

Gnomad4 AMR exome

AF:

0.00201

AC:

AN:

12938

Gnomad4 ASJ exome

AF:

0.000909

AC:

AN:

14298

Gnomad4 EAS exome

AF:

0.00144

AC:

AN:

24286

Gnomad4 SAS exome

AF:

0.00148

AC:

AN:

22962

Gnomad4 FIN exome

AF:

0.00531

AC:

111

AN:

20920

Gnomad4 NFE exome

AF:

0.00247

AC:

1411

AN:

571870

Gnomad4 Remaining exome

AF:

0.00273

AC:

AN:

30744

Heterozygous variant carriers

149

224

298

373

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

108

162

216

270

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

AC:

0.0101957

AN:

0.0101957

Gnomad4 AMR

AF:

0.00523

AC:

0.00522912

AN:

0.00522912

Gnomad4 ASJ

AF:

0.000582

AC:

0.000581734

AN:

0.000581734

Gnomad4 EAS

AF:

0.00421

AC:

0.00421348

AN:

0.00421348

Gnomad4 SAS

AF:

0.00133

AC:

0.00132802

AN:

0.00132802

Gnomad4 FIN

AF:

0.0174

AC:

0.0173982

AN:

0.0173982

Gnomad4 NFE

AF:

0.00393

AC:

0.00392978

AN:

0.00392978

Gnomad4 OTH

AF:

0.00700

AC:

0.007

AN:

0.007

Heterozygous variant carriers

121

161

201

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00500

Hom.:

967

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

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Nov 01, 2022

CeGaT Center for Human Genetics Tuebingen

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

SLC16A1: BS2 -

not specified

Uncertain:1

Nov 11, 2019

Genetic Services Laboratory, University of Chicago

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Mutation Taster

=100/0

polymorphism

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