rs10118570

Variant names:

• chr9-125714185-G-A
• rs10118570

Your query was ambiguous. Multiple possible variants found:

• chr9-125714185-G-A
• chr9-125714185-G-C
• chr9-125714185-G-T

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 0.723 in 152,120 control chromosomes in the GnomAD database, including 40,574 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 0.72 (40574 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 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: 0.723 AC: 109923 AN: 152002 Hom.: 40521 Cov.: 33

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.723 AC: 110042 AN: 152120 Hom.: 40574 Cov.: 33 AF XY: 0.728 AC XY: 54165 AN XY: 74380

African (AFR) AF: 0.851 AC: 35335 AN: 41510

American (AMR) AF: 0.729 AC: 11136 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2124 AN: 3466

East Asian (EAS) AF: 0.771 AC: 3994 AN: 5180

South Asian (SAS) AF: 0.698 AC: 3365 AN: 4818

European-Finnish (FIN) AF: 0.763 AC: 8062 AN: 10570

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43584 AN: 67984

Other (OTH) AF: 0.720 AC: 1523 AN: 2114

Alfa AF: 0.666 Hom.: 137776

Bravo AF: 0.728

Asia WGS AF: 0.742 AC: 2583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.93
DANN	Benign	0.62
PhyloP100		-0.13

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: rs10118570;

hg19: chr9-128476464;