chr9-5277261-G-A

Variant names:

• chr9-5277261-G-A
• rs2146043

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 0.147 in 152,108 control chromosomes in the GnomAD database, including 2,036 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 0.15 (2036 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 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: 0.147 AC: 22341 AN: 151990 Hom.: 2036 Cov.: 32

Gnomad AFR AF: 0.0795

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.147 AC: 22336 AN: 152108 Hom.: 2036 Cov.: 32 AF XY: 0.148 AC XY: 11009 AN XY: 74352

African (AFR) AF: 0.0792 AC: 3290 AN: 41530

American (AMR) AF: 0.245 AC: 3741 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 815 AN: 3470

East Asian (EAS) AF: 0.319 AC: 1654 AN: 5178

South Asian (SAS) AF: 0.165 AC: 798 AN: 4822

European-Finnish (FIN) AF: 0.118 AC: 1248 AN: 10566

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10175 AN: 67964

Other (OTH) AF: 0.190 AC: 400 AN: 2106

Alfa AF: 0.157 Hom.: 3228

Bravo AF: 0.157

Asia WGS AF: 0.226 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.4
DANN	Benign	0.84
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs2146043; hg19: chr9-5277261; COSMIC: COSV60323965;