9-12319300-G-A

Variant names:

• chr9-12319300-G-A
• rs10960592

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 0.268 in 152,050 control chromosomes in the GnomAD database, including 5,458 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 0.27 (5458 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40758 AN: 151932 Hom.: 5461 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.268 AC: 40764 AN: 152050 Hom.: 5458 Cov.: 32 AF XY: 0.265 AC XY: 19676 AN XY: 74348

African (AFR) AF: 0.254 AC: 10531 AN: 41480

American (AMR) AF: 0.227 AC: 3459 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1361 AN: 3464

East Asian (EAS) AF: 0.126 AC: 651 AN: 5162

South Asian (SAS) AF: 0.331 AC: 1599 AN: 4824

European-Finnish (FIN) AF: 0.245 AC: 2596 AN: 10580

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19650 AN: 67956

Other (OTH) AF: 0.270 AC: 570 AN: 2110

Alfa AF: 0.283 Hom.: 27105

Bravo AF: 0.265

Asia WGS AF: 0.238 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.045
DANN	Benign	0.57
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10960592; hg19: chr9-12319300;