rs2104769

Variant names:

• chr9-12240496-A-G
• rs2104769

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;