rs10817669

chr9-114720735-G-Achr9-114720735-G-T

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 0.663 in 152,002 control chromosomes in the GnomAD database, including 34,536 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 0.66 (34536 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 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: 0.663 AC: 100686 AN: 151882 Hom.: 34529 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.663 AC: 100736 AN: 152002 Hom.: 34536 Cov.: 32 AF XY: 0.671 AC XY: 49825 AN XY: 74292

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.719

Gnomad4 OTH AF: 0.652

Alfa AF: 0.708 Hom.: 50100

Bravo AF: 0.647

Asia WGS AF: 0.780 AC: 2702 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.0
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10817669; hg19: chr9-117483015; COSMIC: COSV60395498;