rs3794260

Positions:

• chr12-108204497-G-A

Variant summary

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

The NM_014653.4(WSCD2):​c.383-1792G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.017 in 152,214 control chromosomes in the GnomAD database, including 97 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 0.017 (97 hom., cov: 32)
• Consequence: WSCD2 NM_014653.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.773

Genes affected

WSCD2 (HGNC:29117): (WSC domain containing 2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LOC124903077 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WSCD2	NM_014653.4	c.383-1792G>A		intron_variant		ENST00000547525.6
LOC124903077	XR_007063583.1	n.183-13478C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WSCD2	ENST00000547525.6	c.383-1792G>A		intron_variant		1	NM_014653.4	P1
WSCD2	ENST00000332082.8	c.383-1792G>A		intron_variant		1		P1
WSCD2	ENST00000549903.1	c.383-1792G>A		intron_variant		5
WSCD2	ENST00000551638.5	c.-77-1792G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0170 AC: 2583 AN: 152096 Hom.: 94 Cov.: 32

Gnomad AFR AF: 0.0147

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0121

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.0737

Gnomad FIN AF: 0.00283

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00731

Gnomad OTH AF: 0.0163

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0170 AC: 2594 AN: 152214 Hom.: 97 Cov.: 32 AF XY: 0.0183 AC XY: 1363 AN XY: 74416

Gnomad4 AFR AF: 0.0150

Gnomad4 AMR AF: 0.0121

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.0733

Gnomad4 FIN AF: 0.00283

Gnomad4 NFE AF: 0.00731

Gnomad4 OTH AF: 0.0156

Alfa AF: 0.0110 Hom.: 14

Bravo AF: 0.0167

Asia WGS AF: 0.0940 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.58

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: rs3794260; hg19: chr12-108598274;