9-114720735-G-A

Variant names:

• chr9-114720735-G-A
• rs10817669

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 0.663 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.477 AC: 19798 AN: 41468

American (AMR) AF: 0.697 AC: 10650 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2482 AN: 3470

East Asian (EAS) AF: 0.832 AC: 4258 AN: 5116

South Asian (SAS) AF: 0.814 AC: 3875 AN: 4760

European-Finnish (FIN) AF: 0.803 AC: 8509 AN: 10596

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48875 AN: 67984

Other (OTH) AF: 0.652 AC: 1379 AN: 2114

Alfa AF: 0.700 Hom.: 62429

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
PhyloP100		-0.43

Splicing

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

Other links and lift over

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