rs4234840

Variant names:

• chr4-4915784-A-G
• rs4234840

Your query was ambiguous. Multiple possible variants found:

• chr4-4915784-A-G
• chr4-4915784-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;