rs7739

Positions:

• chr2-174559701-G-A
• chr2-174559701-G-C
• chr2-174559701-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001375834.1(WIPF1):​c.*2846C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.914 in 152,514 control chromosomes in the GnomAD database, including 63,914 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 0.91 (63754 hom., cov: 30)
  • Exomes 𝑓: 0.94 (160 hom.)
• Consequence: WIPF1 NM_001375834.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55

Genes affected

WIPF1 (HGNC:12736): (WAS/WASL interacting protein family member 1) This gene encodes a protein that plays an important role in the organization of the actin cytoskeleton. The encoded protein binds to a region of Wiskott-Aldrich syndrome protein that is frequently mutated in Wiskott-Aldrich syndrome, an X-linked recessive disorder. Impairment of the interaction between these two proteins may contribute to the disease. Two transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WIPF1	NM_001375834.1	c.*2846C>T		3_prime_UTR_variant	8/8	ENST00000679041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WIPF1	ENST00000679041.1	c.*2846C>T		3_prime_UTR_variant	8/8		NM_001375834.1	P3
	ENST00000442996.1	n.217+12224G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.914 AC: 138999 AN: 152032 Hom.: 63716 Cov.: 30

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.961

Gnomad MID AF: 0.818

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.904

GnomAD4 exome AF: 0.937 AC: 341 AN: 364 Hom.: 160 Cov.: 0 AF XY: 0.932 AC XY: 207 AN XY: 222

Gnomad4 FIN exome AF: 0.936

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.914 AC: 139089 AN: 152150 Hom.: 63754 Cov.: 30 AF XY: 0.914 AC XY: 67953 AN XY: 74374

Gnomad4 AFR AF: 0.853

Gnomad4 AMR AF: 0.930

Gnomad4 ASJ AF: 0.938

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.961

Gnomad4 NFE AF: 0.943

Gnomad4 OTH AF: 0.901

Alfa AF: 0.935 Hom.: 56954

Bravo AF: 0.912

Asia WGS AF: 0.828 AC: 2878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	14
DANN	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7739; hg19: chr2-175424429;