9-21241490-A-G

Variant names:

• chr9-21241490-A-G
• rs12551190

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 0.208 in 152,148 control chromosomes in the GnomAD database, including 3,591 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 0.21 (3591 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 1 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 = 0.385 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: 0.208 AC: 31605 AN: 152030 Hom.: 3588 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.208 AC: 31640 AN: 152148 Hom.: 3591 Cov.: 32 AF XY: 0.209 AC XY: 15536 AN XY: 74384

African (AFR) AF: 0.251 AC: 10426 AN: 41496

American (AMR) AF: 0.251 AC: 3834 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 696 AN: 3472

East Asian (EAS) AF: 0.399 AC: 2060 AN: 5162

South Asian (SAS) AF: 0.113 AC: 543 AN: 4824

European-Finnish (FIN) AF: 0.190 AC: 2016 AN: 10590

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11454 AN: 68000

Other (OTH) AF: 0.204 AC: 429 AN: 2108

Alfa AF: 0.189 Hom.: 377

Bravo AF: 0.217

Asia WGS AF: 0.247 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.60
PhyloP100		-0.031

Splicing

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

Other links and lift over

dbSNP: rs12551190; hg19: chr9-21241489;