rs4861040

Variant names:

• chr4-42837237-G-A
• rs4861040

Your query was ambiguous. Multiple possible variants found:

• chr4-42837237-G-A
• chr4-42837237-G-C

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 0.83 in 152,014 control chromosomes in the GnomAD database, including 53,621 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 0.83 (53621 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.922 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: 0.830 AC: 126071 AN: 151896 Hom.: 53604 Cov.: 30

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.830 AC: 126136 AN: 152014 Hom.: 53621 Cov.: 30 AF XY: 0.834 AC XY: 61946 AN XY: 74308

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.880

Gnomad4 ASJ AF: 0.922

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.945

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.911

Gnomad4 OTH AF: 0.844

Alfa AF: 0.902 Hom.: 126094

Bravo AF: 0.817

Asia WGS AF: 0.906 AC: 3151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.96
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4861040; hg19: chr4-42839254;