rs6473015

Variant names:

• chr8-77266249-A-C
• rs6473015

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 0.232 in 152,032 control chromosomes in the GnomAD database, including 4,476 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 0.23 (4476 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 42 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.283 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: 0.232 AC: 35277 AN: 151916 Hom.: 4475 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.232 AC: 35286 AN: 152032 Hom.: 4476 Cov.: 32 AF XY: 0.233 AC XY: 17297 AN XY: 74292

African (AFR) AF: 0.133 AC: 5503 AN: 41530

American (AMR) AF: 0.246 AC: 3747 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 888 AN: 3470

East Asian (EAS) AF: 0.197 AC: 1017 AN: 5160

South Asian (SAS) AF: 0.286 AC: 1377 AN: 4818

European-Finnish (FIN) AF: 0.215 AC: 2276 AN: 10590

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19457 AN: 67904

Other (OTH) AF: 0.248 AC: 523 AN: 2108

Alfa AF: 0.272 Hom.: 25661

Bravo AF: 0.228

Asia WGS AF: 0.238 AC: 832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.71
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs6473015; hg19: chr8-78178485;