7-29881908-G-C

Position:

• chr7-29881908-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080529.3(WIPF3):​c.356-1942G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0249 in 152,250 control chromosomes in the GnomAD database, including 86 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 0.025 (86 hom., cov: 33)
• Consequence: WIPF3 NM_001080529.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WIPF3	NM_001080529.3	c.356-1942G>C		intron_variant		ENST00000242140.10
WIPF3	NM_001391973.1	c.356-1942G>C		intron_variant
WIPF3	XM_017012522.2	c.323-1942G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WIPF3	ENST00000242140.10	c.356-1942G>C		intron_variant		5	NM_001080529.3	P5
WIPF3	ENST00000409123.5	c.356-1942G>C		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.0249 AC: 3790 AN: 152132 Hom.: 86 Cov.: 33

Gnomad AFR AF: 0.00676

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0288

Gnomad ASJ AF: 0.0328

Gnomad EAS AF: 0.0761

Gnomad SAS AF: 0.0350

Gnomad FIN AF: 0.0325

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0292

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0249 AC: 3791 AN: 152250 Hom.: 86 Cov.: 33 AF XY: 0.0249 AC XY: 1853 AN XY: 74434

Gnomad4 AFR AF: 0.00679

Gnomad4 AMR AF: 0.0288

Gnomad4 ASJ AF: 0.0328

Gnomad4 EAS AF: 0.0761

Gnomad4 SAS AF: 0.0350

Gnomad4 FIN AF: 0.0325

Gnomad4 NFE AF: 0.0292

Gnomad4 OTH AF: 0.0247

Alfa AF: 0.00571 Hom.: 2

Bravo AF: 0.0250

Asia WGS AF: 0.0460 AC: 162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.42

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: rs740145; hg19: chr7-29921524;