rs2104769

Variant names:

• chr9-12240496-A-G
• rs2104769

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.134 AC: 5556 AN: 41542

American (AMR) AF: 0.365 AC: 5572 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1673 AN: 3462

East Asian (EAS) AF: 0.161 AC: 826 AN: 5144

South Asian (SAS) AF: 0.300 AC: 1444 AN: 4810

European-Finnish (FIN) AF: 0.398 AC: 4203 AN: 10564

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33844 AN: 67976

Other (OTH) AF: 0.376 AC: 794 AN: 2110

Alfa AF: 0.408 Hom.: 1818

Bravo AF: 0.344

Asia WGS AF: 0.215 AC: 754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.17
DANN	Benign	0.22
PhyloP100		0.0080

Splicing

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

Other links and lift over

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