Genetic Variant NM_015253.2:c.259A>G (chr17-6080917-A-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate

The NM_015253.2(WSCD1):c.259A>G(p.Met87Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000694 in 1,441,826 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

WSCD1
NM_015253.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.201

Publications

0 publications found

Variant links:

Genes affected

WSCD1 (HGNC:29060): (WSC domain containing 1) Predicted to enable sulfotransferase activity. Predicted to be located in membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

WSCD1 links:

ENSG00000285471 (HGNC:):

ENSG00000285471 links:

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ACMG classification

Classification was made for transcript

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=0.07945499).

BP6

Variant 17-6080917-A-G is Benign according to our data. Variant chr17-6080917-A-G is described in ClinVar as Likely_benign. ClinVar VariationId is 3190820.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015253.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
WSCD1	NM_015253.2	MANE Select	c.259A>G	p.Met87Val	missense	Exon 2 of 9	NP_056068.1	Q658N2
WSCD1	NM_001388405.1		c.259A>G	p.Met87Val	missense	Exon 2 of 9	NP_001375334.1	Q658N2
WSCD1	NM_001388406.1		c.259A>G	p.Met87Val	missense	Exon 2 of 9	NP_001375335.1	Q658N2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
WSCD1	ENST00000317744.10	TSL:1 MANE Select	c.259A>G	p.Met87Val	missense	Exon 2 of 9	ENSP00000323087.5	Q658N2
WSCD1	ENST00000573634.5	TSL:1	c.80-7073A>G		intron	N/A	ENSP00000460396.1	I3L3E6
WSCD1	ENST00000920366.1		c.259A>G	p.Met87Val	missense	Exon 3 of 11	ENSP00000590425.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

6.94e-7

AC:

AN:

1441826

Hom.:

Cov.:

AF XY:

0.00000140

AC XY:

AN XY:

716382

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33376

American (AMR)

AF:

0.0000234

AC:

AN:

42788

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25694

East Asian (EAS)

AF:

0.00

AC:

AN:

39206

South Asian (SAS)

AF:

0.00

AC:

AN:

83932

European-Finnish (FIN)

AF:

0.00

AC:

AN:

44514

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5654

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1106844

Other (OTH)

AF:

0.00

AC:

AN:

59818

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.052

BayesDel_addAF

Benign

-0.13

BayesDel_noAF

Benign

-0.43

CADD

Benign

0.022

(source)

DANN

Benign

0.28

DEOGEN2

Benign

0.0024

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.0017

LIST_S2

Benign

0.52

M_CAP

Uncertain

0.15

MetaRNN

Benign

0.041

MetaSVM

Benign

-0.96

MutationAssessor

Benign

-0.35

PhyloP100

-0.20

PrimateAI

Uncertain

0.57

PROVEAN

Benign

-0.050

REVEL

Benign

0.22

Sift

Benign

0.29

Sift4G

Benign

0.78

Polyphen

0.0

Vest4

0.053

MutPred

0.18

Gain of sheet (P = 0.0477)

MVP

0.13

MPC

0.25

ClinPred

0.067

GERP RS

-2.3

Varity_R

0.057

gMVP

0.46

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over