9-5191128-A-G

Variant names:

• chr9-5191128-A-G
• rs7850294

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 0.421 in 152,074 control chromosomes in the GnomAD database, including 16,920 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 0.42 (16920 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63878 AN: 151956 Hom.: 16879 Cov.: 32

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.421 AC: 63977 AN: 152074 Hom.: 16920 Cov.: 32 AF XY: 0.418 AC XY: 31055 AN XY: 74322

African (AFR) AF: 0.761 AC: 31591 AN: 41492

American (AMR) AF: 0.341 AC: 5202 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 889 AN: 3470

East Asian (EAS) AF: 0.246 AC: 1274 AN: 5184

South Asian (SAS) AF: 0.344 AC: 1650 AN: 4802

European-Finnish (FIN) AF: 0.320 AC: 3376 AN: 10562

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18859 AN: 67976

Other (OTH) AF: 0.380 AC: 802 AN: 2112

Alfa AF: 0.349 Hom.: 3119

Bravo AF: 0.431

Asia WGS AF: 0.336 AC: 1165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.5
DANN	Benign	0.55
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs7850294; hg19: chr9-5191128;