7-29874853-A-T

Position:

• chr7-29874853-A-T

Variant summary

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

The NM_001080529.3(WIPF3):​c.91-977A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,072 control chromosomes in the GnomAD database, including 7,567 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 0.30 (7567 hom., cov: 32)
• Consequence: WIPF3 NM_001080529.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WIPF3	NM_001080529.3	c.91-977A>T		intron_variant		ENST00000242140.10	NP_001073998.2
WIPF3	NM_001391973.1	c.91-977A>T		intron_variant			NP_001378902.1
WIPF3	XM_017012522.2	c.58-977A>T		intron_variant			XP_016868011.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WIPF3	ENST00000242140.10	c.91-977A>T		intron_variant		5	NM_001080529.3	ENSP00000242140.6
WIPF3	ENST00000409123.5	c.91-977A>T		intron_variant		5		ENSP00000386790.1

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46261 AN: 151954 Hom.: 7543 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.0204

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.305 AC: 46319 AN: 152072 Hom.: 7567 Cov.: 32 AF XY: 0.299 AC XY: 22249 AN XY: 74338

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.0203

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.297

Alfa AF: 0.165 Hom.: 343

Bravo AF: 0.306

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.59

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: rs6974174; hg19: chr7-29914469;