9-12187104-A-G

Variant names:

• chr9-12187104-A-G
• rs1416572

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 0.692 in 151,834 control chromosomes in the GnomAD database, including 36,901 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 0.69 (36901 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 4 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 = 0.737 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.692 AC: 104949 AN: 151716 Hom.: 36882 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.692 AC: 105013 AN: 151834 Hom.: 36901 Cov.: 32 AF XY: 0.685 AC XY: 50793 AN XY: 74188

African (AFR) AF: 0.674 AC: 27939 AN: 41432

American (AMR) AF: 0.606 AC: 9214 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2759 AN: 3460

East Asian (EAS) AF: 0.381 AC: 1957 AN: 5134

South Asian (SAS) AF: 0.623 AC: 3001 AN: 4820

European-Finnish (FIN) AF: 0.690 AC: 7276 AN: 10546

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50449 AN: 67912

Other (OTH) AF: 0.687 AC: 1451 AN: 2112

Alfa AF: 0.716 Hom.: 30433

Bravo AF: 0.683

Asia WGS AF: 0.470 AC: 1639 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.39
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs1416572; hg19: chr9-12187104;