Variant rs782052199 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_004694.5(SLC16A6):c.1552G>C(p.Val518Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000044 in 1,364,840 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 28)

Exomes 𝑓: 0.0000044 ( 0 hom. )

Consequence

SLC16A6
NM_004694.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.32

Variant links:

Genes affected

SLC16A6 (HGNC:10927): (solute carrier family 16 member 6) Predicted to enable monocarboxylic acid transmembrane transporter activity. Predicted to be involved in monocarboxylic acid transport. Predicted to be located in membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC16A6 links:

ARSG (HGNC:24102): (arylsulfatase G) The protein encoded by this gene belongs to the sulfatase enzyme family. Sulfatases hydrolyze sulfate esters from sulfated steroids, carbohydrates, proteoglycans, and glycolipids. They are involved in hormone biosynthesis, modulation of cell signaling, and degradation of macromolecules. This protein displays arylsulfatase activity at acidic pH, as is typical of lysosomal sulfatases, and has been shown to localize in the lysosomes. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2012]

ARSG links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.056895167).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A6	NM_004694.5 link	c.1552G>C	p.Val518Leu	missense_variant	Exon 6 of 6	ENST00000580666.6	NP_004685.2	O15403A0A024R8J3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC16A6	ENST00000580666.6 link	c.1552G>C	p.Val518Leu	missense_variant	Exon 6 of 6	1	NM_004694.5	ENSP00000462985.1	O15403
SLC16A6	ENST00000327268.8 link	c.1552G>C	p.Val518Leu	missense_variant	Exon 7 of 7	1		ENSP00000319991.4	O15403
ARSG	ENST00000448504.6 link	c.-552+9690C>G		intron_variant	Intron 1 of 11	1		ENSP00000407193.2	Q96EG1
ARSG	ENST00000578726.1 link	n.27-4774C>G		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000440

AC:

AN:

1364840

Hom.:

Cov.:

AF XY:

0.00000299

AC XY:

AN XY:

668758

show subpopulations

Gnomad4 AFR exome

AF:

0.0000999

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000187

Gnomad4 OTH exome

AF:

0.0000178

GnomAD4 genome

Cov.:

Bravo

AF:

0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.076

BayesDel_addAF

Benign

-0.36

BayesDel_noAF

Benign

-0.75

CADD

Benign

3.6

DANN

Benign

0.81

DEOGEN2

Benign

0.012

T;T;.

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.11

LIST_S2

Benign

0.52

.;T;T

M_CAP

Benign

0.0045

MetaRNN

Benign

0.057

T;T;T

MetaSVM

Benign

-0.94

MutationAssessor

Benign

1.1

L;L;.

PrimateAI

Benign

0.29

PROVEAN

Benign

-0.39

N;.;.

REVEL

Benign

0.013

Sift

Benign

0.27

T;.;.

Sift4G

Benign

0.78

T;T;T

Polyphen

0.0020

B;B;.

Vest4

0.031

MutPred

0.24

Loss of sheet (P = 0.0315);Loss of sheet (P = 0.0315);.;

MVP

0.040

MPC

1.8

ClinPred

0.11

GERP RS

-6.0

Varity_R

0.043

gMVP

0.19

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over