rs402841

Variant names:

• chr4-170560296-G-A
• rs402841

Your query was ambiguous. Multiple possible variants found:

• chr4-170560296-G-A
• chr4-170560296-G-C
• chr4-170560296-G-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 0.509 in 152,126 control chromosomes in the GnomAD database, including 23,864 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 0.51 (23864 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.778
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77465 AN: 152006 Hom.: 23863 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.509 AC: 77473 AN: 152126 Hom.: 23864 Cov.: 33 AF XY: 0.518 AC XY: 38559 AN XY: 74368

African (AFR) AF: 0.166 AC: 6898 AN: 41484

American (AMR) AF: 0.421 AC: 6437 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1999 AN: 3470

East Asian (EAS) AF: 0.820 AC: 4244 AN: 5178

South Asian (SAS) AF: 0.670 AC: 3236 AN: 4832

European-Finnish (FIN) AF: 0.794 AC: 8407 AN: 10582

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44409 AN: 67978

Other (OTH) AF: 0.518 AC: 1090 AN: 2106

Alfa AF: 0.459 Hom.: 1809

Bravo AF: 0.467

Asia WGS AF: 0.732 AC: 2540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.69
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs402841; hg19: chr4-171481447;