chr5-170820294-G-A

Position:

• chr5-170820294-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.428 in 152,034 control chromosomes in the GnomAD database, including 15,789 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 0.43 (15789 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64993 AN: 151916 Hom.: 15779 Cov.: 33

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.428 AC: 65010 AN: 152034 Hom.: 15789 Cov.: 33 AF XY: 0.434 AC XY: 32252 AN XY: 74328

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.472

Alfa AF: 0.456 Hom.: 7645

Bravo AF: 0.422

Asia WGS AF: 0.635 AC: 2209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	17
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1363281; hg19: chr5-170247298;