rs3744725

Variant names:

• chr17-6122560-C-T
• rs3744725
• NM_015253.2:c.*1899C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015253.2(WSCD1):​c.*1899C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,208 control chromosomes in the GnomAD database, including 3,327 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.20 (3327 hom., cov: 33)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: WSCD1 NM_015253.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WSCD1	NM_015253.2	c.*1899C>T		3_prime_UTR_variant	Exon 9 of 9	ENST00000317744.10	NP_056068.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WSCD1	ENST00000317744.10	c.*1899C>T		3_prime_UTR_variant	Exon 9 of 9	1	NM_015253.2	ENSP00000323087.5
WSCD1	ENST00000574946.5	c.*1899C>T		3_prime_UTR_variant	Exon 9 of 9	2		ENSP00000460825.1

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29680 AN: 152036 Hom.: 3330 Cov.: 33

Gnomad AFR AF: 0.0949

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.222

GnomAD4 exome AF: 0.130 AC: 7 AN: 54 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 3 AN XY: 30

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.175

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.195 AC: 29672 AN: 152154 Hom.: 3327 Cov.: 33 AF XY: 0.198 AC XY: 14710 AN XY: 74378

Gnomad4 AFR AF: 0.0948

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.220

Alfa AF: 0.224 Hom.: 3665

Bravo AF: 0.195

Asia WGS AF: 0.282 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
DANN	Benign	0.48

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

LitVar

Other links and lift over

dbSNP: rs3744725; hg19: chr17-6025880;