rs4834009

chr4-124921001-C-Achr4-124921001-C-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 0.943 in 152,168 control chromosomes in the GnomAD database, including 67,696 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 0.94 (67696 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.95 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: 0.943 AC: 143397 AN: 152050 Hom.: 67646 Cov.: 32

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.949

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.944

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

GnomAD4 genome AF: 0.943 AC: 143501 AN: 152168 Hom.: 67696 Cov.: 32 AF XY: 0.941 AC XY: 69994 AN XY: 74382

Gnomad4 AFR AF: 0.958

Gnomad4 AMR AF: 0.920

Gnomad4 ASJ AF: 0.949

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.869

Gnomad4 FIN AF: 0.967

Gnomad4 NFE AF: 0.942

Gnomad4 OTH AF: 0.937

Alfa AF: 0.944 Hom.: 6567

Bravo AF: 0.942

Asia WGS AF: 0.907 AC: 3142 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.71
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: rs4834009; hg19: chr4-125842156;