chr9-4976029-A-G

Variant names:

• chr9-4976029-A-G
• rs7864782

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 0.376 in 151,890 control chromosomes in the GnomAD database, including 11,113 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 0.38 (11113 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57169 AN: 151772 Hom.: 11114 Cov.: 31

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.376 AC: 57185 AN: 151890 Hom.: 11113 Cov.: 31 AF XY: 0.372 AC XY: 27631 AN XY: 74210

African (AFR) AF: 0.307 AC: 12720 AN: 41408

American (AMR) AF: 0.411 AC: 6272 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1650 AN: 3470

East Asian (EAS) AF: 0.172 AC: 890 AN: 5178

South Asian (SAS) AF: 0.264 AC: 1269 AN: 4804

European-Finnish (FIN) AF: 0.414 AC: 4363 AN: 10530

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28813 AN: 67920

Other (OTH) AF: 0.371 AC: 781 AN: 2104

Alfa AF: 0.396 Hom.: 2077

Bravo AF: 0.376

Asia WGS AF: 0.227 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.69
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs7864782; hg19: chr9-4976029; COSMIC: COSV69444393;