9-19189215-C-A

Variant names:

• chr9-19189215-C-A
• rs12551120

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 0.241 in 151,986 control chromosomes in the GnomAD database, including 5,035 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 0.24 (5035 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.930
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 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: 0.241 AC: 36625 AN: 151868 Hom.: 5030 Cov.: 31

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.241 AC: 36641 AN: 151986 Hom.: 5035 Cov.: 31 AF XY: 0.237 AC XY: 17614 AN XY: 74298

African (AFR) AF: 0.141 AC: 5845 AN: 41462

American (AMR) AF: 0.251 AC: 3818 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 820 AN: 3468

East Asian (EAS) AF: 0.0259 AC: 134 AN: 5180

South Asian (SAS) AF: 0.258 AC: 1239 AN: 4808

European-Finnish (FIN) AF: 0.219 AC: 2315 AN: 10564

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21410 AN: 67952

Other (OTH) AF: 0.282 AC: 593 AN: 2106

Alfa AF: 0.285 Hom.: 3864

Bravo AF: 0.238

Asia WGS AF: 0.170 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.49
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs12551120; hg19: chr9-19189213;