9-12281247-G-T

Variant names:

• chr9-12281247-G-T
• rs10960562

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 0.173 in 151,880 control chromosomes in the GnomAD database, including 2,710 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 0.17 (2710 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 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: 0.173 AC: 26290 AN: 151764 Hom.: 2713 Cov.: 32

Gnomad AFR AF: 0.0654

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.205

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.173 AC: 26289 AN: 151880 Hom.: 2710 Cov.: 32 AF XY: 0.173 AC XY: 12818 AN XY: 74210

African (AFR) AF: 0.0654 AC: 2709 AN: 41436

American (AMR) AF: 0.129 AC: 1962 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1049 AN: 3464

East Asian (EAS) AF: 0.163 AC: 842 AN: 5154

South Asian (SAS) AF: 0.337 AC: 1621 AN: 4816

European-Finnish (FIN) AF: 0.173 AC: 1816 AN: 10498

Middle Eastern (MID) AF: 0.179 AC: 52 AN: 290

European-Non Finnish (NFE) AF: 0.230 AC: 15640 AN: 67948

Other (OTH) AF: 0.178 AC: 376 AN: 2112

Alfa AF: 0.126 Hom.: 289

Bravo AF: 0.162

Asia WGS AF: 0.238 AC: 829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.33
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs10960562; hg19: chr9-12281247;