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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.794

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.518

Alfa AF: 0.482 Hom.: 1801

Bravo AF: 0.467

Asia WGS AF: 0.732 AC: 2540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs402841; hg19: chr4-171481447;