rs200168065

Variant names:

• chr17-68271390-A-C
• rs200168065
• NM_004694.5:c.770T>G

Your query was ambiguous. Multiple possible variants found:

• chr17-68271390-A-C
• chr17-68271390-A-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_004694.5(SLC16A6):​c.770T>G​(p.Leu257Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 32)
• Consequence: SLC16A6 NM_004694.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390

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]

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]

ACMG classification

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=0.06712279).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A6	NM_004694.5	c.770T>G	p.Leu257Arg	missense_variant	Exon 5 of 6	ENST00000580666.6	NP_004685.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC16A6	ENST00000580666.6	c.770T>G	p.Leu257Arg	missense_variant	Exon 5 of 6	1	NM_004694.5	ENSP00000462985.1
SLC16A6	ENST00000327268.8	c.770T>G	p.Leu257Arg	missense_variant	Exon 6 of 7	1		ENSP00000319991.4
ARSG	ENST00000448504.6	c.-552+11964A>C		intron_variant	Intron 1 of 11	1		ENSP00000407193.2
ARSG	ENST00000578726.1	n.27-2500A>C		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.066
BayesDel_addAF	Benign	-0.32	T
BayesDel_noAF	Benign	-0.70
CADD	Benign	0.037
DANN	Benign	0.45
DEOGEN2	Benign	0.081	T;T;.
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.020	N
LIST_S2	Benign	0.24	.;T;T
M_CAP	Benign	0.0031	T
MetaRNN	Benign	0.067	T;T;T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	0.60	N;N;.
PrimateAI	Benign	0.21	T
PROVEAN	Benign	0.55	N;.;.
REVEL	Benign	0.012
Sift	Benign	0.31	T;.;.
Sift4G	Benign	0.54	T;T;T
Polyphen		0.0010	B;B;.
Vest4		0.048
MutPred		0.44		Gain of methylation at K262 (P = 0.0503);Gain of methylation at K262 (P = 0.0503);Gain of methylation at K262 (P = 0.0503);
MVP		0.28
MPC		0.67
ClinPred		0.13	T
GERP RS		-2.1
Varity_R		0.068
gMVP		0.41

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs200168065; hg19: chr17-66267531;