rs10509897

Variant names:

• chr10-109471430-C-T
• rs10509897

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 0.162 in 151,910 control chromosomes in the GnomAD database, including 6,272 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 0.16 (6272 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 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: 0.162 AC: 24583 AN: 151794 Hom.: 6237 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0663

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0394

Gnomad FIN AF: 0.000757

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.00820

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.162 AC: 24668 AN: 151910 Hom.: 6272 Cov.: 32 AF XY: 0.157 AC XY: 11655 AN XY: 74280

African (AFR) AF: 0.546 AC: 22580 AN: 41350

American (AMR) AF: 0.0661 AC: 1010 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3466

East Asian (EAS) AF: 0.00213 AC: 11 AN: 5166

South Asian (SAS) AF: 0.0383 AC: 185 AN: 4824

European-Finnish (FIN) AF: 0.000757 AC: 8 AN: 10568

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.00820 AC: 557 AN: 67948

Other (OTH) AF: 0.121 AC: 255 AN: 2112

Alfa AF: 0.0979 Hom.: 454

Bravo AF: 0.185

Asia WGS AF: 0.0650 AC: 225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.8
DANN	Benign	0.23
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs10509897; hg19: chr10-111231188;