chr9-30979642-A-G

Variant names:

• chr9-30979642-A-G
• rs2888998

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 0.194 in 152,024 control chromosomes in the GnomAD database, including 3,940 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 0.19 (3940 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.881
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 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: 0.194 AC: 29399 AN: 151904 Hom.: 3934 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.194 AC: 29421 AN: 152024 Hom.: 3940 Cov.: 32 AF XY: 0.203 AC XY: 15055 AN XY: 74298

African (AFR) AF: 0.226 AC: 9391 AN: 41480

American (AMR) AF: 0.299 AC: 4556 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3470

East Asian (EAS) AF: 0.720 AC: 3715 AN: 5160

South Asian (SAS) AF: 0.244 AC: 1176 AN: 4812

European-Finnish (FIN) AF: 0.164 AC: 1739 AN: 10574

Middle Eastern (MID) AF: 0.247 AC: 71 AN: 288

European-Non Finnish (NFE) AF: 0.114 AC: 7776 AN: 67968

Other (OTH) AF: 0.200 AC: 422 AN: 2114

Alfa AF: 0.146 Hom.: 5056

Bravo AF: 0.211

Asia WGS AF: 0.447 AC: 1536 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.68
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs2888998; hg19: chr9-30979640;