chr9-12582565-C-T

Variant names:

• chr9-12582565-C-T
• rs1325154

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 0.911 in 151,710 control chromosomes in the GnomAD database, including 63,110 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 0.91 (63110 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.939 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: 0.911 AC: 138164 AN: 151592 Hom.: 63072 Cov.: 31

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.914

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

GnomAD4 genome AF: 0.911 AC: 138260 AN: 151710 Hom.: 63110 Cov.: 31 AF XY: 0.906 AC XY: 67178 AN XY: 74150

African (AFR) AF: 0.947 AC: 39251 AN: 41466

American (AMR) AF: 0.896 AC: 13608 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.887 AC: 3074 AN: 3464

East Asian (EAS) AF: 0.804 AC: 4128 AN: 5136

South Asian (SAS) AF: 0.759 AC: 3659 AN: 4818

European-Finnish (FIN) AF: 0.905 AC: 9587 AN: 10596

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.914 AC: 61920 AN: 67726

Other (OTH) AF: 0.912 AC: 1921 AN: 2106

Alfa AF: 0.911 Hom.: 273081

Bravo AF: 0.916

Asia WGS AF: 0.757 AC: 2634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.17
DANN	Benign	0.42
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1325154; hg19: chr9-12582565;