rs10453196

Variant names:

• chr9-25966742-G-A
• rs10453196

Your query was ambiguous. Multiple possible variants found:

• chr9-25966742-G-A
• chr9-25966742-G-C

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 0.137 in 151,738 control chromosomes in the GnomAD database, including 2,949 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 0.14 (2949 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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: 0.137 AC: 20697 AN: 151620 Hom.: 2923 Cov.: 30

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0630

Gnomad ASJ AF: 0.0699

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.0493

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0318

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.137 AC: 20762 AN: 151738 Hom.: 2949 Cov.: 30 AF XY: 0.138 AC XY: 10247 AN XY: 74180

African (AFR) AF: 0.358 AC: 14746 AN: 41246

American (AMR) AF: 0.0629 AC: 958 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0699 AC: 242 AN: 3462

East Asian (EAS) AF: 0.160 AC: 825 AN: 5148

South Asian (SAS) AF: 0.213 AC: 1022 AN: 4800

European-Finnish (FIN) AF: 0.0493 AC: 521 AN: 10558

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0318 AC: 2163 AN: 67976

Other (OTH) AF: 0.121 AC: 254 AN: 2106

Alfa AF: 0.0492 Hom.: 496

Bravo AF: 0.145

Asia WGS AF: 0.183 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.90
DANN	Benign	0.27
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10453196; hg19: chr9-25966740;