rs4834009

Variant names:

• chr4-124921001-C-A
• rs4834009

Your query was ambiguous. Multiple possible variants found:

• chr4-124921001-C-A
• chr4-124921001-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.958 AC: 39799 AN: 41558

American (AMR) AF: 0.920 AC: 14059 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.949 AC: 3290 AN: 3468

East Asian (EAS) AF: 0.943 AC: 4886 AN: 5182

South Asian (SAS) AF: 0.869 AC: 4188 AN: 4820

European-Finnish (FIN) AF: 0.967 AC: 10255 AN: 10600

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.942 AC: 63964 AN: 67936

Other (OTH) AF: 0.937 AC: 1979 AN: 2112

Alfa AF: 0.943 Hom.: 18033

Bravo AF: 0.942

Asia WGS AF: 0.907 AC: 3142 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.71
DANN	Benign	0.54
PhyloP100		-0.082

Splicing

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

Other links and lift over

dbSNP: rs4834009; hg19: chr4-125842156;