rs10481715

Variant names:

• chr9-91548484-G-A
• rs10481715

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 0.088 in 152,144 control chromosomes in the GnomAD database, including 652 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 0.088 (652 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.866
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 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: 0.0878 AC: 13346 AN: 152026 Hom.: 638 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.0667

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0866

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0693

Gnomad OTH AF: 0.0865

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

GnomAD4 genome AF: 0.0880 AC: 13393 AN: 152144 Hom.: 652 Cov.: 32 AF XY: 0.0908 AC XY: 6750 AN XY: 74380

African (AFR) AF: 0.122 AC: 5081 AN: 41518

American (AMR) AF: 0.0666 AC: 1018 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0548 AC: 190 AN: 3468

East Asian (EAS) AF: 0.137 AC: 705 AN: 5150

South Asian (SAS) AF: 0.108 AC: 523 AN: 4824

European-Finnish (FIN) AF: 0.0866 AC: 917 AN: 10588

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0693 AC: 4710 AN: 67986

Other (OTH) AF: 0.0922 AC: 195 AN: 2114

Alfa AF: 0.0717 Hom.: 681

Bravo AF: 0.0865

Asia WGS AF: 0.149 AC: 519 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	1.7
DANN	Benign	0.40
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs10481715; hg19: chr9-94310766;