rs402841

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;