rs1895910

Variant names:

• chr12-108180501-T-G
• rs1895910
• NM_014653.4:c.-551-14781T>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.-551-14781T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,232 control chromosomes in the GnomAD database, including 2,522 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 0.16 (2522 hom., cov: 33)
• Consequence: WSCD2 NM_014653.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391
• Publications: 2 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.219 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WSCD2	NM_014653.4	MANE Select	c.-551-14781T>G		intron	N/A	NP_055468.2
	WSCD2	NM_001304447.2		c.-552+12920T>G		intron	N/A	NP_001291376.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WSCD2	ENST00000547525.6	TSL:1 MANE Select	c.-551-14781T>G		intron	N/A	ENSP00000448047.1
	WSCD2	ENST00000332082.8	TSL:1	c.-552+12920T>G		intron	N/A	ENSP00000331933.4
	WSCD2	ENST00000551638.5	TSL:4	c.-77-25788T>G		intron	N/A	ENSP00000446744.1

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24084 AN: 152114 Hom.: 2524 Cov.: 33

Gnomad AFR AF: 0.0408

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.158 AC: 24075 AN: 152232 Hom.: 2522 Cov.: 33 AF XY: 0.158 AC XY: 11790 AN XY: 74408

African (AFR) AF: 0.0406 AC: 1689 AN: 41558

American (AMR) AF: 0.174 AC: 2656 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 600 AN: 3472

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5190

South Asian (SAS) AF: 0.122 AC: 591 AN: 4826

European-Finnish (FIN) AF: 0.258 AC: 2732 AN: 10584

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15085 AN: 67990

Other (OTH) AF: 0.140 AC: 295 AN: 2102

Alfa AF: 0.201 Hom.: 4635

Bravo AF: 0.145

Asia WGS AF: 0.0630 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.71
PhyloP100		-0.39
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: rs1895910; hg19: chr12-108574278;