9-25449124-T-C

Variant names:

• chr9-25449124-T-C
• rs12552736

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;