9-117684548-C-T

Variant names:

• chr9-117684548-C-T
• rs1928298

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 0.527 in 151,698 control chromosomes in the GnomAD database, including 23,738 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 0.53 (23738 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.662 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: 0.528 AC: 80010 AN: 151580 Hom.: 23744 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.527 AC: 80018 AN: 151698 Hom.: 23738 Cov.: 32 AF XY: 0.526 AC XY: 38999 AN XY: 74134

African (AFR) AF: 0.234 AC: 9690 AN: 41414

American (AMR) AF: 0.586 AC: 8906 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2134 AN: 3458

East Asian (EAS) AF: 0.618 AC: 3157 AN: 5110

South Asian (SAS) AF: 0.612 AC: 2956 AN: 4828

European-Finnish (FIN) AF: 0.554 AC: 5861 AN: 10582

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45230 AN: 67798

Other (OTH) AF: 0.571 AC: 1199 AN: 2098

Alfa AF: 0.634 Hom.: 15797

Bravo AF: 0.520

Asia WGS AF: 0.589 AC: 2050 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.45
DANN	Benign	0.44
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1928298; hg19: chr9-120446826;