chr12-108204497-G-A

Variant names:

• chr12-108204497-G-A
• rs3794260
• NM_014653.4:c.383-1792G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 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.383-1792G>A		intron	N/A	NP_055468.2
	WSCD2	NM_001304447.2		c.383-1792G>A		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.383-1792G>A		intron	N/A	ENSP00000448047.1
	WSCD2	ENST00000332082.8	TSL:1	c.383-1792G>A		intron	N/A	ENSP00000331933.4
	WSCD2	ENST00000549903.1	TSL:5	c.383-1792G>A		intron	N/A	ENSP00000447272.1

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

African (AFR) AF: 0.0150 AC: 623 AN: 41536

American (AMR) AF: 0.0121 AC: 185 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0216 AC: 75 AN: 3470

East Asian (EAS) AF: 0.153 AC: 789 AN: 5162

South Asian (SAS) AF: 0.0733 AC: 353 AN: 4816

European-Finnish (FIN) AF: 0.00283 AC: 30 AN: 10598

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00731 AC: 497 AN: 68024

Other (OTH) AF: 0.0156 AC: 33 AN: 2110

Alfa AF: 0.0112 Hom.: 21

Bravo AF: 0.0167

Asia WGS AF: 0.0940 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.58
PhyloP100		-0.77
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: rs3794260; hg19: chr12-108598274;