rs12552736

chr9-25449124-T-Cchr9-25449124-T-G

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 0.115 in 152,132 control chromosomes in the GnomAD database, including 1,420 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 0.12 (1420 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.753

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17520 AN: 152014 Hom.: 1410 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0452

Gnomad EAS AF: 0.0172

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.0628

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0776

Gnomad OTH AF: 0.0920

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

GnomAD4 genome AF: 0.115 AC: 17563 AN: 152132 Hom.: 1420 Cov.: 32 AF XY: 0.111 AC XY: 8286 AN XY: 74380

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0452

Gnomad4 EAS AF: 0.0172

Gnomad4 SAS AF: 0.0242

Gnomad4 FIN AF: 0.0628

Gnomad4 NFE AF: 0.0776

Gnomad4 OTH AF: 0.0910

Alfa AF: 0.0770 Hom.: 799

Bravo AF: 0.126

Asia WGS AF: 0.0370 AC: 129 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.6
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12552736; hg19: chr9-25449122;