chr9-79730966-G-A

Variant names:

• chr9-79730966-G-A
• rs2151145

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 0.787 in 152,220 control chromosomes in the GnomAD database, including 47,348 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 0.79 (47348 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.811 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: 0.787 AC: 119745 AN: 152102 Hom.: 47297 Cov.: 33

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.787 AC: 119855 AN: 152220 Hom.: 47348 Cov.: 33 AF XY: 0.789 AC XY: 58697 AN XY: 74416

African (AFR) AF: 0.736 AC: 30579 AN: 41528

American (AMR) AF: 0.821 AC: 12558 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2536 AN: 3468

East Asian (EAS) AF: 0.828 AC: 4277 AN: 5168

South Asian (SAS) AF: 0.832 AC: 4021 AN: 4832

European-Finnish (FIN) AF: 0.790 AC: 8382 AN: 10606

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.806 AC: 54804 AN: 68006

Other (OTH) AF: 0.789 AC: 1663 AN: 2108

Alfa AF: 0.798 Hom.: 115532

Bravo AF: 0.785

Asia WGS AF: 0.820 AC: 2851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.71
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs2151145; hg19: chr9-82345881;