rs10504711

Variant names:

• chr8-79576017-C-A
• rs10504711

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 0.027 in 152,222 control chromosomes in the GnomAD database, including 216 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 0.027 (216 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 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: 0.0270 AC: 4110 AN: 152104 Hom.: 219 Cov.: 32

Gnomad AFR AF: 0.00881

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0809

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.0946

Gnomad FIN AF: 0.00538

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0118

Gnomad OTH AF: 0.0229

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

GnomAD4 genome AF: 0.0270 AC: 4105 AN: 152222 Hom.: 216 Cov.: 32 AF XY: 0.0304 AC XY: 2261 AN XY: 74438

African (AFR) AF: 0.00883 AC: 367 AN: 41544

American (AMR) AF: 0.0809 AC: 1236 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0159 AC: 55 AN: 3468

East Asian (EAS) AF: 0.206 AC: 1067 AN: 5174

South Asian (SAS) AF: 0.0940 AC: 454 AN: 4828

European-Finnish (FIN) AF: 0.00538 AC: 57 AN: 10600

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0118 AC: 803 AN: 68004

Other (OTH) AF: 0.0232 AC: 49 AN: 2114

Alfa AF: 0.0190 Hom.: 133

Bravo AF: 0.0313

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.70
DANN	Benign	0.36
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs10504711; hg19: chr8-80488252;