rs6473164

Variant names:

• chr8-79492467-G-A
• rs6473164

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 0.529 in 151,972 control chromosomes in the GnomAD database, including 22,357 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 0.53 (22357 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 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: 0.529 AC: 80367 AN: 151854 Hom.: 22310 Cov.: 32

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.529 AC: 80469 AN: 151972 Hom.: 22357 Cov.: 32 AF XY: 0.527 AC XY: 39119 AN XY: 74252

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.533

Alfa AF: 0.513 Hom.: 2777

Bravo AF: 0.532

Asia WGS AF: 0.521 AC: 1812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6473164; hg19: chr8-80404702;