rs4864029

Positions:

• chr4-131103329-G-A
• chr4-131103329-G-C
• chr4-131103329-G-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 0.854 in 151,802 control chromosomes in the GnomAD database, including 55,850 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 0.85 (55850 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.907 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: 0.855 AC: 129646 AN: 151694 Hom.: 55839 Cov.: 30

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.936

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.854 AC: 129701 AN: 151802 Hom.: 55850 Cov.: 30 AF XY: 0.852 AC XY: 63182 AN XY: 74146

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.920

Gnomad4 ASJ AF: 0.936

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.815

Gnomad4 NFE AF: 0.906

Gnomad4 OTH AF: 0.878

Alfa AF: 0.901 Hom.: 83944

Bravo AF: 0.857

Asia WGS AF: 0.876 AC: 3047 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	1.9
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4864029; hg19: chr4-132024484;