rs10885459

Variant names:

• chr10-113450166-G-C
• rs10885459

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 0.221 in 152,042 control chromosomes in the GnomAD database, including 3,998 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 0.22 (3998 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.26 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: 0.221 AC: 33547 AN: 151924 Hom.: 3998 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.221 AC: 33552 AN: 152042 Hom.: 3998 Cov.: 32 AF XY: 0.218 AC XY: 16202 AN XY: 74306

African (AFR) AF: 0.159 AC: 6582 AN: 41476

American (AMR) AF: 0.190 AC: 2909 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1120 AN: 3472

East Asian (EAS) AF: 0.272 AC: 1405 AN: 5174

South Asian (SAS) AF: 0.172 AC: 831 AN: 4820

European-Finnish (FIN) AF: 0.230 AC: 2434 AN: 10582

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17447 AN: 67926

Other (OTH) AF: 0.254 AC: 535 AN: 2108

Alfa AF: 0.240 Hom.: 640

Bravo AF: 0.216

Asia WGS AF: 0.216 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.4
DANN	Benign	0.48
PhyloP100		0.0080

Splicing

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

Other links and lift over

dbSNP: rs10885459; hg19: chr10-115209925;