rs6473164

Variant names:

• chr8-79492467-G-A
• rs6473164

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 0.529 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.696 AC: 28835 AN: 41454

American (AMR) AF: 0.420 AC: 6406 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1926 AN: 3470

East Asian (EAS) AF: 0.404 AC: 2085 AN: 5162

South Asian (SAS) AF: 0.582 AC: 2803 AN: 4820

European-Finnish (FIN) AF: 0.417 AC: 4394 AN: 10546

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32248 AN: 67944

Other (OTH) AF: 0.533 AC: 1127 AN: 2114

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6473164; hg19: chr8-80404702;