rs7313402

Variant names:

• chr12-108209193-C-A
• rs7313402
• NM_014653.4:c.498-928C>A

Your query was ambiguous. Multiple possible variants found:

• chr12-108209193-C-A
• chr12-108209193-C-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014653.4(WSCD2):​c.498-928C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,920 control chromosomes in the GnomAD database, including 17,991 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 0.48 (17991 hom., cov: 32)
• Consequence: WSCD2 NM_014653.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• Publications: 6 publications found

Genes affected

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

ENSG00000307044 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014653.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WSCD2	NM_014653.4	MANE Select	c.498-928C>A		intron	N/A	NP_055468.2
	WSCD2	NM_001304447.2		c.498-928C>A		intron	N/A	NP_001291376.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WSCD2	ENST00000547525.6	TSL:1 MANE Select	c.498-928C>A		intron	N/A	ENSP00000448047.1
	WSCD2	ENST00000332082.8	TSL:1	c.498-928C>A		intron	N/A	ENSP00000331933.4
	WSCD2	ENST00000549903.1	TSL:5	c.498-928C>A		intron	N/A	ENSP00000447272.1

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73428 AN: 151804 Hom.: 17972 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.484 AC: 73488 AN: 151920 Hom.: 17991 Cov.: 32 AF XY: 0.489 AC XY: 36269 AN XY: 74240

African (AFR) AF: 0.433 AC: 17917 AN: 41384

American (AMR) AF: 0.522 AC: 7962 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1847 AN: 3468

East Asian (EAS) AF: 0.597 AC: 3071 AN: 5146

South Asian (SAS) AF: 0.506 AC: 2441 AN: 4822

European-Finnish (FIN) AF: 0.536 AC: 5655 AN: 10560

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 32995 AN: 67956

Other (OTH) AF: 0.473 AC: 1000 AN: 2112

Alfa AF: 0.484 Hom.: 53184

Bravo AF: 0.479

Asia WGS AF: 0.568 AC: 1976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.9
DANN	Benign	0.81
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7313402; hg19: chr12-108602970;