9-108693295-A-G

Variant names:

• chr9-108693295-A-G
• rs10512385

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 0.15 in 152,234 control chromosomes in the GnomAD database, including 1,979 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 0.15 (1979 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 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: 0.150 AC: 22772 AN: 152116 Hom.: 1977 Cov.: 33

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0840

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0569

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.150 AC: 22795 AN: 152234 Hom.: 1979 Cov.: 33 AF XY: 0.151 AC XY: 11250 AN XY: 74432

African (AFR) AF: 0.240 AC: 9948 AN: 41522

American (AMR) AF: 0.0837 AC: 1280 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 573 AN: 3472

East Asian (EAS) AF: 0.0565 AC: 293 AN: 5188

South Asian (SAS) AF: 0.161 AC: 773 AN: 4816

European-Finnish (FIN) AF: 0.173 AC: 1835 AN: 10604

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7695 AN: 68024

Other (OTH) AF: 0.144 AC: 305 AN: 2114

Alfa AF: 0.123 Hom.: 2458

Bravo AF: 0.145

Asia WGS AF: 0.123 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	15
DANN	Benign	0.72
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs10512385; hg19: chr9-111455575;