17-68271611-G-A

Variant names:

• chr17-68271611-G-A
• rs62087130
• NM_004694.5:c.549C>T

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_004694.5(SLC16A6):​c.549C>T​(p.Leu183Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00581 in 1,613,962 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0037 (3 hom., cov: 32)
  • Exomes 𝑓: 0.0060 (36 hom.)
• Consequence: SLC16A6 NM_004694.5 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.168

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

Our verdict: Benign. The variant received -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BP6: Variant 17-68271611-G-A is Benign according to our data. Variant chr17-68271611-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2648150.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.168 with no splicing effect.
• BS2: High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A6	NM_004694.5	c.549C>T	p.Leu183Leu	synonymous_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.549C>T	p.Leu183Leu	synonymous_variant	Exon 5 of 6	1	NM_004694.5	ENSP00000462985.1

Frequencies

GnomAD3 genomes AF: 0.00374 AC: 569 AN: 152212 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.00101

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00255

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00217

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00667

Gnomad OTH AF: 0.00239

GnomAD2 exomes AF: 0.00418 AC: 1051 AN: 251274 AF XY: 0.00409

Gnomad AFR exome AF: 0.00154

Gnomad AMR exome AF: 0.00148

Gnomad ASJ exome AF: 0.00109

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00217

Gnomad NFE exome AF: 0.00762

Gnomad OTH exome AF: 0.00392

GnomAD4 exome AF: 0.00603 AC: 8809 AN: 1461632 Hom.: 36 Cov.: 33 AF XY: 0.00580 AC XY: 4215 AN XY: 727052

Gnomad4 AFR exome AF: 0.00117 AC: 39 AN: 33476

Gnomad4 AMR exome AF: 0.00152 AC: 68 AN: 44720

Gnomad4 ASJ exome AF: 0.000804 AC: 21 AN: 26132

Gnomad4 EAS exome AF: 0.0000252 AC: 1 AN: 39696

Gnomad4 SAS exome AF: 0.000870 AC: 75 AN: 86256

Gnomad4 FIN exome AF: 0.00242 AC: 129 AN: 53416

Gnomad4 NFE exome AF: 0.00729 AC: 8103 AN: 1111774

Gnomad4 Remaining exome AF: 0.00598 AC: 361 AN: 60394

GnomAD4 genome AF: 0.00374 AC: 569 AN: 152330 Hom.: 3 Cov.: 32 AF XY: 0.00320 AC XY: 238 AN XY: 74482

Gnomad4 AFR AF: 0.00101 AC: 0.00101025 AN: 0.00101025

Gnomad4 AMR AF: 0.00255 AC: 0.00254902 AN: 0.00254902

Gnomad4 ASJ AF: 0.000865 AC: 0.000864553 AN: 0.000864553

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.000415 AC: 0.000414766 AN: 0.000414766

Gnomad4 FIN AF: 0.00217 AC: 0.00216573 AN: 0.00216573

Gnomad4 NFE AF: 0.00667 AC: 0.00667353 AN: 0.00667353

Gnomad4 OTH AF: 0.00236 AC: 0.00236295 AN: 0.00236295

Alfa AF: 0.00544 Hom.: 4

Bravo AF: 0.00402

Asia WGS AF: 0.000577 AC: 2 AN: 3478

EpiCase AF: 0.00654

EpiControl AF: 0.00652

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Apr 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

SLC16A6: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	5.6
DANN	Benign	0.85
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs62087130; hg19: chr17-66267752;