chr9-12301585-T-G

Variant names:

• chr9-12301585-T-G
• rs10511572

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 0.078 in 151,966 control chromosomes in the GnomAD database, including 1,391 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 0.078 (1391 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.249 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: 0.0778 AC: 11816 AN: 151848 Hom.: 1388 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0327

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.0301

Gnomad SAS AF: 0.0191

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00586

Gnomad OTH AF: 0.0566

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

GnomAD4 genome AF: 0.0780 AC: 11847 AN: 151966 Hom.: 1391 Cov.: 32 AF XY: 0.0752 AC XY: 5585 AN XY: 74298

African (AFR) AF: 0.253 AC: 10504 AN: 41462

American (AMR) AF: 0.0327 AC: 498 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 51 AN: 3460

East Asian (EAS) AF: 0.0302 AC: 156 AN: 5164

South Asian (SAS) AF: 0.0191 AC: 92 AN: 4820

European-Finnish (FIN) AF: 0.00179 AC: 19 AN: 10620

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00586 AC: 398 AN: 67880

Other (OTH) AF: 0.0579 AC: 122 AN: 2108

Alfa AF: 0.0564 Hom.: 111

Bravo AF: 0.0872

Asia WGS AF: 0.0550 AC: 191 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	1.1
DANN	Benign	0.74
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs10511572; hg19: chr9-12301585;