9-12912862-T-G

Variant names:

• chr9-12912862-T-G
• rs12553535

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 0.21 in 152,158 control chromosomes in the GnomAD database, including 3,896 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 0.21 (3896 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31920 AN: 152040 Hom.: 3889 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.210 AC: 31936 AN: 152158 Hom.: 3896 Cov.: 32 AF XY: 0.212 AC XY: 15742 AN XY: 74408

African (AFR) AF: 0.117 AC: 4856 AN: 41528

American (AMR) AF: 0.343 AC: 5237 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1222 AN: 3468

East Asian (EAS) AF: 0.354 AC: 1829 AN: 5170

South Asian (SAS) AF: 0.241 AC: 1159 AN: 4814

European-Finnish (FIN) AF: 0.145 AC: 1540 AN: 10594

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15262 AN: 67994

Other (OTH) AF: 0.232 AC: 488 AN: 2106

Alfa AF: 0.228 Hom.: 2543

Bravo AF: 0.224

Asia WGS AF: 0.277 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.070
DANN	Benign	0.70
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs12553535; hg19: chr9-12912861;