chr12-9218736-C-T

Position:

• chr12-9218736-C-T

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 0.804 in 152,150 control chromosomes in the GnomAD database, including 49,341 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 0.80 (49341 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122273 AN: 152032 Hom.: 49287 Cov.: 33

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.850

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.804 AC: 122382 AN: 152150 Hom.: 49341 Cov.: 33 AF XY: 0.804 AC XY: 59836 AN XY: 74390

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.862

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.883

Gnomad4 SAS AF: 0.741

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.817

Gnomad4 OTH AF: 0.823

Alfa AF: 0.818 Hom.: 116283

Bravo AF: 0.811

Asia WGS AF: 0.830 AC: 2887 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	0.58
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6487679; hg19: chr12-9371332;