9-79339083-G-A

Variant names:

• chr9-79339083-G-A
• rs7849719

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 0.232 in 151,856 control chromosomes in the GnomAD database, including 4,202 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 0.23 (4202 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.314 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: 0.232 AC: 35245 AN: 151738 Hom.: 4196 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.232 AC: 35261 AN: 151856 Hom.: 4202 Cov.: 32 AF XY: 0.235 AC XY: 17438 AN XY: 74208

African (AFR) AF: 0.273 AC: 11305 AN: 41394

American (AMR) AF: 0.209 AC: 3187 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 609 AN: 3468

East Asian (EAS) AF: 0.289 AC: 1490 AN: 5152

South Asian (SAS) AF: 0.327 AC: 1579 AN: 4824

European-Finnish (FIN) AF: 0.234 AC: 2465 AN: 10518

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.204 AC: 13867 AN: 67932

Other (OTH) AF: 0.200 AC: 421 AN: 2102

Alfa AF: 0.212 Hom.: 15087

Bravo AF: 0.233

Asia WGS AF: 0.279 AC: 968 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.96
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs7849719; hg19: chr9-81953998;