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. The variant received -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. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L257P) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC16A6 NM_004694.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390
• Publications: 0 publications found

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]

ARSG Gene-Disease associations (from GenCC):

• Usher syndrome, type 4

  Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp
• Usher syndrome type 3

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.06712279).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004694.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A6	NM_004694.5	MANE Select	c.770T>G	p.Leu257Arg	missense	Exon 5 of 6	NP_004685.2
	SLC16A6	NM_001174166.2		c.770T>G	p.Leu257Arg	missense	Exon 6 of 7	NP_001167637.1	O15403
	ARSG	NM_014960.5		c.-552+11964A>C		intron	N/A	NP_055775.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A6	ENST00000580666.6	TSL:1 MANE Select	c.770T>G	p.Leu257Arg	missense	Exon 5 of 6	ENSP00000462985.1	O15403
	SLC16A6	ENST00000327268.8	TSL:1	c.770T>G	p.Leu257Arg	missense	Exon 6 of 7	ENSP00000319991.4	O15403
	ARSG	ENST00000448504.6	TSL:1	c.-552+11964A>C		intron	N/A	ENSP00000407193.2	Q96EG1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.020	N
LIST_S2	Benign	0.24	T
M_CAP	Benign	0.0031	T
MetaRNN	Benign	0.067	T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	0.60	N
PhyloP100		-0.39
PrimateAI	Benign	0.21	T
PROVEAN	Benign	0.55	N
REVEL	Benign	0.012
Sift	Benign	0.31	T
Sift4G	Benign	0.54	T
Polyphen		0.0010	B
Vest4		0.048
MutPred		0.44		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

Other links and lift over

dbSNP: rs200168065; hg19: chr17-66267531;