chr9-76995712-T-C

Variant names:

• chr9-76995712-T-C
• rs79460104

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 0.0837 in 151,452 control chromosomes in the GnomAD database, including 925 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 0.084 (925 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 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: 0.0837 AC: 12665 AN: 151334 Hom.: 925 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.00881

Gnomad AMR AF: 0.0790

Gnomad ASJ AF: 0.0413

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.0456

Gnomad FIN AF: 0.0717

Gnomad MID AF: 0.0419

Gnomad NFE AF: 0.0263

Gnomad OTH AF: 0.0659

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

GnomAD4 genome AF: 0.0837 AC: 12680 AN: 151452 Hom.: 925 Cov.: 32 AF XY: 0.0842 AC XY: 6237 AN XY: 74070

African (AFR) AF: 0.177 AC: 7314 AN: 41272

American (AMR) AF: 0.0789 AC: 1202 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0413 AC: 143 AN: 3460

East Asian (EAS) AF: 0.216 AC: 1097 AN: 5068

South Asian (SAS) AF: 0.0454 AC: 217 AN: 4780

European-Finnish (FIN) AF: 0.0717 AC: 757 AN: 10562

Middle Eastern (MID) AF: 0.0313 AC: 9 AN: 288

European-Non Finnish (NFE) AF: 0.0263 AC: 1786 AN: 67780

Other (OTH) AF: 0.0699 AC: 147 AN: 2102

Alfa AF: 0.445 Hom.: 6684

Bravo AF: 0.0888

Asia WGS AF: 0.122 AC: 423 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	2.7
DANN	Benign	0.39
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs79460104; hg19: chr9-79610628;