9-12240496-A-G

Position:

• chr9-12240496-A-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 0.357 in 152,074 control chromosomes in the GnomAD database, including 11,688 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 0.36 (11688 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 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: 0.357 AC: 54276 AN: 151956 Hom.: 11695 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.357 AC: 54272 AN: 152074 Hom.: 11688 Cov.: 32 AF XY: 0.351 AC XY: 26052 AN XY: 74326

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.376

Alfa AF: 0.419 Hom.: 1805

Bravo AF: 0.344

Asia WGS AF: 0.215 AC: 754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.17
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2104769; hg19: chr9-12240496; COSMIC: COSV69448000;