9-117530056-C-T

Variant names:

• chr9-117530056-C-T
• rs1985317

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 0.482 in 152,032 control chromosomes in the GnomAD database, including 19,786 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 0.48 (19786 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.609 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: 0.483 AC: 73300 AN: 151914 Hom.: 19785 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.482 AC: 73316 AN: 152032 Hom.: 19786 Cov.: 32 AF XY: 0.483 AC XY: 35881 AN XY: 74314

African (AFR) AF: 0.267 AC: 11071 AN: 41462

American (AMR) AF: 0.389 AC: 5944 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1855 AN: 3470

East Asian (EAS) AF: 0.241 AC: 1244 AN: 5160

South Asian (SAS) AF: 0.472 AC: 2276 AN: 4820

European-Finnish (FIN) AF: 0.696 AC: 7358 AN: 10570

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41744 AN: 67962

Other (OTH) AF: 0.475 AC: 1004 AN: 2112

Alfa AF: 0.558 Hom.: 108151

Bravo AF: 0.444

Asia WGS AF: 0.352 AC: 1229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.31
PhyloP100		0.076

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1985317;

hg19: chr9-120292334;