10-95574534-C-A

Variant names:

• chr10-95574534-C-A
• rs526928

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 0.385 in 152,038 control chromosomes in the GnomAD database, including 13,721 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 0.38 (13721 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 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: 0.385 AC: 58471 AN: 151920 Hom.: 13723 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.385 AC: 58472 AN: 152038 Hom.: 13721 Cov.: 32 AF XY: 0.385 AC XY: 28595 AN XY: 74300

African (AFR) AF: 0.104 AC: 4305 AN: 41492

American (AMR) AF: 0.490 AC: 7482 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1111 AN: 3466

East Asian (EAS) AF: 0.544 AC: 2811 AN: 5170

South Asian (SAS) AF: 0.351 AC: 1692 AN: 4818

European-Finnish (FIN) AF: 0.515 AC: 5431 AN: 10552

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34365 AN: 67960

Other (OTH) AF: 0.356 AC: 753 AN: 2114

Alfa AF: 0.436 Hom.: 5455

Bravo AF: 0.374

Asia WGS AF: 0.429 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.2
DANN	Benign	0.43
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs526928; hg19: chr10-97334291;