9-7909576-G-T

Variant names:

• chr9-7909576-G-T
• rs7849795

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 0.818 in 152,080 control chromosomes in the GnomAD database, including 51,367 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 0.82 (51367 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 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: 0.817 AC: 124215 AN: 151962 Hom.: 51303 Cov.: 32

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.818 AC: 124341 AN: 152080 Hom.: 51367 Cov.: 32 AF XY: 0.815 AC XY: 60577 AN XY: 74294

African (AFR) AF: 0.935 AC: 38815 AN: 41518

American (AMR) AF: 0.781 AC: 11932 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2361 AN: 3470

East Asian (EAS) AF: 0.939 AC: 4848 AN: 5162

South Asian (SAS) AF: 0.825 AC: 3976 AN: 4820

European-Finnish (FIN) AF: 0.745 AC: 7866 AN: 10560

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.764 AC: 51897 AN: 67970

Other (OTH) AF: 0.794 AC: 1672 AN: 2106

Alfa AF: 0.773 Hom.: 74300

Bravo AF: 0.826

Asia WGS AF: 0.885 AC: 3078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.51
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs7849795; hg19: chr9-7909576;