rs4234840

chr4-4915784-A-Gchr4-4915784-A-T

Variant summary

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

The variant allele was found at a frequency of 0.721 in 152,004 control chromosomes in the GnomAD database, including 39,786 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 0.72 (39786 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109524 AN: 151884 Hom.: 39748 Cov.: 31

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.721 AC: 109623 AN: 152004 Hom.: 39786 Cov.: 31 AF XY: 0.731 AC XY: 54311 AN XY: 74302

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.902

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.763

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.726

Alfa AF: 0.694 Hom.: 18098

Bravo AF: 0.720

Asia WGS AF: 0.840 AC: 2922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.11
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4234840; hg19: chr4-4917511;