10-8524545-T-C

Variant names:

• chr10-8524545-T-C
• rs2765399

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 0.587 in 151,676 control chromosomes in the GnomAD database, including 26,629 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 0.59 (26629 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.725
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.693 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: 0.587 AC: 88963 AN: 151558 Hom.: 26615 Cov.: 31

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.587 AC: 89022 AN: 151676 Hom.: 26629 Cov.: 31 AF XY: 0.590 AC XY: 43727 AN XY: 74114

African (AFR) AF: 0.453 AC: 18737 AN: 41356

American (AMR) AF: 0.634 AC: 9660 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2271 AN: 3470

East Asian (EAS) AF: 0.712 AC: 3648 AN: 5124

South Asian (SAS) AF: 0.685 AC: 3294 AN: 4810

European-Finnish (FIN) AF: 0.645 AC: 6777 AN: 10502

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42754 AN: 67872

Other (OTH) AF: 0.609 AC: 1279 AN: 2100

Alfa AF: 0.612 Hom.: 36084

Bravo AF: 0.579

Asia WGS AF: 0.671 AC: 2332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	17
DANN	Benign	0.47
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs2765399; hg19: chr10-8566508;