7-29874853-A-T

Variant names:

• chr7-29874853-A-T
• rs6974174
• NM_001080529.3:c.91-977A>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.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
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080529.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WIPF3	NM_001080529.3	MANE Select	c.91-977A>T		intron	N/A	NP_001073998.2	A6NGB9
	WIPF3	NM_001391973.1		c.91-977A>T		intron	N/A	NP_001378902.1	A0A0A0MSG0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WIPF3	ENST00000242140.10	TSL:5 MANE Select	c.91-977A>T		intron	N/A	ENSP00000242140.6	A6NGB9
	WIPF3	ENST00000409123.5	TSL:5	c.91-977A>T		intron	N/A	ENSP00000386790.1	A0A0A0MSG0
	WIPF3	ENST00000869766.1		c.91-977A>T		intron	N/A	ENSP00000539825.1

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

African (AFR) AF: 0.403 AC: 16717 AN: 41436

American (AMR) AF: 0.247 AC: 3776 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1221 AN: 3468

East Asian (EAS) AF: 0.0203 AC: 105 AN: 5182

South Asian (SAS) AF: 0.185 AC: 891 AN: 4820

European-Finnish (FIN) AF: 0.262 AC: 2768 AN: 10580

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19806 AN: 67982

Other (OTH) AF: 0.297 AC: 628 AN: 2112

Alfa AF: 0.165 Hom.: 343

Bravo AF: 0.306

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.59
PhyloP100		-0.12
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: rs6974174; hg19: chr7-29914469;