9-12914397-G-T

Variant names:

• chr9-12914397-G-T
• rs1953021

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 0.689 in 151,956 control chromosomes in the GnomAD database, including 36,310 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 0.69 (36310 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.727 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: 0.689 AC: 104617 AN: 151838 Hom.: 36286 Cov.: 31

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.689 AC: 104693 AN: 151956 Hom.: 36310 Cov.: 31 AF XY: 0.693 AC XY: 51499 AN XY: 74260

African (AFR) AF: 0.693 AC: 28707 AN: 41426

American (AMR) AF: 0.636 AC: 9711 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1842 AN: 3460

East Asian (EAS) AF: 0.582 AC: 2992 AN: 5138

South Asian (SAS) AF: 0.747 AC: 3593 AN: 4810

European-Finnish (FIN) AF: 0.817 AC: 8650 AN: 10582

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47169 AN: 67964

Other (OTH) AF: 0.646 AC: 1365 AN: 2112

Alfa AF: 0.689 Hom.: 7774

Bravo AF: 0.670

Asia WGS AF: 0.667 AC: 2318 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.32
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1953021; hg19: chr9-12914396;