rs4861040

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;