7-29881908-G-C

Variant names:

• chr7-29881908-G-C
• rs740145
• NM_001080529.3:c.356-1942G>C

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.91).
• 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 rank	MANE	Protein	UniProt
WIPF3	NM_001080529.3	c.356-1942G>C		intron_variant	Intron 4 of 8	ENST00000242140.10	NP_001073998.2
WIPF3	NM_001391973.1	c.356-1942G>C		intron_variant	Intron 4 of 7		NP_001378902.1
WIPF3	XM_017012522.2	c.323-1942G>C		intron_variant	Intron 3 of 7		XP_016868011.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WIPF3	ENST00000242140.10	c.356-1942G>C		intron_variant	Intron 4 of 8	5	NM_001080529.3	ENSP00000242140.6
WIPF3	ENST00000409123.5	c.356-1942G>C		intron_variant	Intron 4 of 7	5		ENSP00000386790.1

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

African (AFR) AF: 0.00679 AC: 282 AN: 41522

American (AMR) AF: 0.0288 AC: 440 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0328 AC: 114 AN: 3472

East Asian (EAS) AF: 0.0761 AC: 394 AN: 5180

South Asian (SAS) AF: 0.0350 AC: 169 AN: 4830

European-Finnish (FIN) AF: 0.0325 AC: 345 AN: 10608

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0292 AC: 1987 AN: 68020

Other (OTH) AF: 0.0247 AC: 52 AN: 2108

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
PhyloP100		-0.26
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: rs740145; hg19: chr7-29921524;