chr9-21678974-A-G

Variant names:

• chr9-21678974-A-G
• rs7035284

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 0.33 in 151,970 control chromosomes in the GnomAD database, including 10,836 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 0.33 (10836 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.612 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: 0.330 AC: 50043 AN: 151852 Hom.: 10811 Cov.: 33

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.330 AC: 50119 AN: 151970 Hom.: 10836 Cov.: 33 AF XY: 0.329 AC XY: 24416 AN XY: 74278

African (AFR) AF: 0.618 AC: 25596 AN: 41420

American (AMR) AF: 0.268 AC: 4100 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 833 AN: 3470

East Asian (EAS) AF: 0.403 AC: 2089 AN: 5186

South Asian (SAS) AF: 0.267 AC: 1288 AN: 4816

European-Finnish (FIN) AF: 0.246 AC: 2594 AN: 10550

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.187 AC: 12708 AN: 67940

Other (OTH) AF: 0.298 AC: 629 AN: 2112

Alfa AF: 0.270 Hom.: 1095

Bravo AF: 0.348

Asia WGS AF: 0.330 AC: 1128 AN: 3420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.0
DANN	Benign	0.85
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs7035284; hg19: chr9-21678973;