rs10987465

Variant names:

• chr9-126752852-A-T
• rs10987465

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 0.0251 in 152,130 control chromosomes in the GnomAD database, including 391 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 0.025 (391 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 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: 0.0252 AC: 3835 AN: 152012 Hom.: 392 Cov.: 32

Gnomad AFR AF: 0.00317

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0134

Gnomad ASJ AF: 0.0162

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0458

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00782

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0251 AC: 3825 AN: 152130 Hom.: 391 Cov.: 32 AF XY: 0.0301 AC XY: 2235 AN XY: 74350

African (AFR) AF: 0.00316 AC: 131 AN: 41492

American (AMR) AF: 0.0134 AC: 204 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0162 AC: 56 AN: 3466

East Asian (EAS) AF: 0.358 AC: 1847 AN: 5162

South Asian (SAS) AF: 0.109 AC: 522 AN: 4810

European-Finnish (FIN) AF: 0.0458 AC: 486 AN: 10616

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00782 AC: 532 AN: 67992

Other (OTH) AF: 0.0213 AC: 45 AN: 2110

Alfa AF: 0.0119 Hom.: 8

Bravo AF: 0.0214

Asia WGS AF: 0.185 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.78
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs10987465; hg19: chr9-129515131;