12-108241683-G-A

Position:

• chr12-108241683-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.1345+1139G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,064 control chromosomes in the GnomAD database, including 25,914 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 0.58 (25914 hom., cov: 32)
• Consequence: WSCD2 NM_014653.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160

Genes affected

WSCD2 (HGNC:29117): (WSC domain containing 2) 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WSCD2	NM_014653.4	c.1345+1139G>A		intron_variant		ENST00000547525.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WSCD2	ENST00000547525.6	c.1345+1139G>A		intron_variant		1	NM_014653.4	P1
WSCD2	ENST00000332082.8	c.1345+1139G>A		intron_variant		1		P1
WSCD2	ENST00000549903.1	c.1345+1139G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87825 AN: 151946 Hom.: 25900 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.578 AC: 87875 AN: 152064 Hom.: 25914 Cov.: 32 AF XY: 0.573 AC XY: 42575 AN XY: 74304

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.571

Alfa AF: 0.628 Hom.: 30133

Bravo AF: 0.568

Asia WGS AF: 0.555 AC: 1933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.47

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: rs1346173; hg19: chr12-108635460;