rs7795668

Variant names:

• chr7-29850727-A-T
• rs7795668
• NM_001080529.3:c.90+15913A>T

Variant summary

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

The NM_001080529.3(WIPF3):​c.90+15913A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,070 control chromosomes in the GnomAD database, including 3,774 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 0.22 (3774 hom., cov: 32)
• Consequence: WIPF3 NM_001080529.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.575
• Publications: 3 publications found

Genes affected

WIPF3 (HGNC:22004): (WAS/WASL interacting protein family member 3) Predicted to enable SH3 domain binding activity and actin binding activity. Predicted to be involved in actin filament-based movement. Predicted to be located in cytosol. Predicted to be active in actin filament. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WIPF3	NM_001080529.3	c.90+15913A>T		intron_variant	Intron 2 of 8	ENST00000242140.10	NP_001073998.2
WIPF3	NM_001391973.1	c.90+15913A>T		intron_variant	Intron 2 of 7		NP_001378902.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WIPF3	ENST00000242140.10	c.90+15913A>T		intron_variant	Intron 2 of 8	5	NM_001080529.3	ENSP00000242140.6
WIPF3	ENST00000409123.5	c.90+15913A>T		intron_variant	Intron 2 of 7	5		ENSP00000386790.1

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32765 AN: 151952 Hom.: 3764 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.0841

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.216 AC: 32804 AN: 152070 Hom.: 3774 Cov.: 32 AF XY: 0.213 AC XY: 15846 AN XY: 74348

African (AFR) AF: 0.299 AC: 12380 AN: 41442

American (AMR) AF: 0.181 AC: 2767 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 615 AN: 3470

East Asian (EAS) AF: 0.0837 AC: 432 AN: 5160

South Asian (SAS) AF: 0.156 AC: 749 AN: 4808

European-Finnish (FIN) AF: 0.156 AC: 1657 AN: 10606

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13572 AN: 67972

Other (OTH) AF: 0.204 AC: 432 AN: 2114

Alfa AF: 0.215 Hom.: 469

Bravo AF: 0.219

Asia WGS AF: 0.121 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.73
PhyloP100		0.57
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: rs7795668; hg19: chr7-29890343;