chr9-99086304-G-A

Variant names:

• chr9-99086304-G-A
• rs7874183

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 0.282 in 152,154 control chromosomes in the GnomAD database, including 6,778 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 0.28 (6778 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42931 AN: 152036 Hom.: 6775 Cov.: 33

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.282 AC: 42961 AN: 152154 Hom.: 6778 Cov.: 33 AF XY: 0.285 AC XY: 21188 AN XY: 74386

African (AFR) AF: 0.351 AC: 14541 AN: 41476

American (AMR) AF: 0.317 AC: 4852 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 761 AN: 3468

East Asian (EAS) AF: 0.601 AC: 3110 AN: 5174

South Asian (SAS) AF: 0.442 AC: 2132 AN: 4824

European-Finnish (FIN) AF: 0.165 AC: 1752 AN: 10602

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14928 AN: 68006

Other (OTH) AF: 0.301 AC: 635 AN: 2110

Alfa AF: 0.254 Hom.: 7829

Bravo AF: 0.297

Asia WGS AF: 0.497 AC: 1725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.49
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs7874183; hg19: chr9-101848586; COSMIC: COSV60380898;