rs10120953

Variant names:

• chr9-128366600-G-A
• rs10120953

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 0.0244 in 151,232 control chromosomes in the GnomAD database, including 68 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 0.024 (68 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913
• 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 (SAS) allele frequency at 95% confidence interval = 0.0511 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: 0.0244 AC: 3680 AN: 151110 Hom.: 67 Cov.: 32

Gnomad AFR AF: 0.0289

Gnomad AMI AF: 0.00887

Gnomad AMR AF: 0.0156

Gnomad ASJ AF: 0.0627

Gnomad EAS AF: 0.00475

Gnomad SAS AF: 0.0568

Gnomad FIN AF: 0.0323

Gnomad MID AF: 0.0197

Gnomad NFE AF: 0.0198

Gnomad OTH AF: 0.0233

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

GnomAD4 genome AF: 0.0244 AC: 3687 AN: 151232 Hom.: 68 Cov.: 32 AF XY: 0.0254 AC XY: 1877 AN XY: 73874

African (AFR) AF: 0.0290 AC: 1195 AN: 41244

American (AMR) AF: 0.0156 AC: 238 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.0627 AC: 217 AN: 3460

East Asian (EAS) AF: 0.00476 AC: 24 AN: 5042

South Asian (SAS) AF: 0.0566 AC: 270 AN: 4768

European-Finnish (FIN) AF: 0.0323 AC: 339 AN: 10486

Middle Eastern (MID) AF: 0.0213 AC: 6 AN: 282

European-Non Finnish (NFE) AF: 0.0198 AC: 1342 AN: 67752

Other (OTH) AF: 0.0230 AC: 48 AN: 2088

Alfa AF: 0.0235 Hom.: 8

Bravo AF: 0.0222

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.70
DANN	Benign	0.88
PhyloP100		-0.91

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10120953;

hg19: chr9-131128879;