9-12912862-T-G

Variant names:

• chr9-12912862-T-G
• rs12553535

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.210 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

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.232

Alfa AF: 0.227 Hom.: 2305

Bravo AF: 0.224

Asia WGS AF: 0.277 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12553535; hg19: chr9-12912861;