chr9-84212344-A-G

Variant names:

• chr9-84212344-A-G
• rs1932660

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 0.608 in 152,160 control chromosomes in the GnomAD database, including 31,223 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 0.61 (31223 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.904 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: 0.608 AC: 92421 AN: 152042 Hom.: 31149 Cov.: 33

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.608 AC: 92560 AN: 152160 Hom.: 31223 Cov.: 33 AF XY: 0.613 AC XY: 45632 AN XY: 74384

African (AFR) AF: 0.875 AC: 36355 AN: 41538

American (AMR) AF: 0.658 AC: 10058 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1503 AN: 3470

East Asian (EAS) AF: 0.926 AC: 4799 AN: 5184

South Asian (SAS) AF: 0.735 AC: 3549 AN: 4826

European-Finnish (FIN) AF: 0.467 AC: 4927 AN: 10556

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29604 AN: 67988

Other (OTH) AF: 0.580 AC: 1225 AN: 2112

Alfa AF: 0.488 Hom.: 10162

Bravo AF: 0.634

Asia WGS AF: 0.845 AC: 2935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.9
DANN	Benign	0.83
PhyloP100		-0.074

Splicing

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

Other links and lift over

dbSNP: rs1932660; hg19: chr9-86827259;