rs10504605

Variant names:

• chr8-76019658-A-G
• rs10504605

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 0.0545 in 152,158 control chromosomes in the GnomAD database, including 276 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 0.054 (276 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.05
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0684 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: 0.0545 AC: 8282 AN: 152040 Hom.: 275 Cov.: 32

Gnomad AFR AF: 0.0300

Gnomad AMI AF: 0.0485

Gnomad AMR AF: 0.0718

Gnomad ASJ AF: 0.0504

Gnomad EAS AF: 0.0445

Gnomad SAS AF: 0.0207

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0608

Gnomad OTH AF: 0.0646

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

GnomAD4 genome AF: 0.0545 AC: 8287 AN: 152158 Hom.: 276 Cov.: 32 AF XY: 0.0560 AC XY: 4168 AN XY: 74374

African (AFR) AF: 0.0299 AC: 1244 AN: 41554

American (AMR) AF: 0.0719 AC: 1097 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0504 AC: 175 AN: 3470

East Asian (EAS) AF: 0.0446 AC: 230 AN: 5154

South Asian (SAS) AF: 0.0207 AC: 100 AN: 4826

European-Finnish (FIN) AF: 0.103 AC: 1094 AN: 10608

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0609 AC: 4137 AN: 67972

Other (OTH) AF: 0.0639 AC: 135 AN: 2112

Alfa AF: 0.0581 Hom.: 270

Bravo AF: 0.0546

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	17
DANN	Benign	0.78
PhyloP100		3.0

Splicing

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

Other links and lift over

dbSNP: rs10504605; hg19: chr8-76931893;