rs10504601

Variant names:

• chr8-75969256-G-A
• rs10504601

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 0.0786 in 152,086 control chromosomes in the GnomAD database, including 653 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 0.079 (653 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 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: 0.0785 AC: 11923 AN: 151966 Hom.: 651 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0898

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0442

Gnomad SAS AF: 0.0331

Gnomad FIN AF: 0.0213

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0429

Gnomad OTH AF: 0.0895

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

GnomAD4 genome AF: 0.0786 AC: 11947 AN: 152086 Hom.: 653 Cov.: 32 AF XY: 0.0775 AC XY: 5763 AN XY: 74336

African (AFR) AF: 0.151 AC: 6270 AN: 41492

American (AMR) AF: 0.0900 AC: 1372 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 512 AN: 3466

East Asian (EAS) AF: 0.0443 AC: 229 AN: 5172

South Asian (SAS) AF: 0.0332 AC: 160 AN: 4826

European-Finnish (FIN) AF: 0.0213 AC: 226 AN: 10604

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0430 AC: 2919 AN: 67958

Other (OTH) AF: 0.0885 AC: 187 AN: 2112

Alfa AF: 0.0634 Hom.: 1108

Bravo AF: 0.0897

Asia WGS AF: 0.0520 AC: 179 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	14
DANN	Benign	0.59
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10504601; hg19: chr8-76881491;