rs10481715

chr9-91548484-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0666

Gnomad4 ASJ AF: 0.0548

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0866

Gnomad4 NFE AF: 0.0693

Gnomad4 OTH AF: 0.0922

Alfa AF: 0.0705 Hom.: 530

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10481715; hg19: chr9-94310766;