rs10758939

Variant names:

• chr9-8125410-A-G
• rs10758939

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 0.551 in 151,916 control chromosomes in the GnomAD database, including 25,971 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 0.55 (25971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.684 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: 0.552 AC: 83752 AN: 151798 Hom.: 25973 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.551 AC: 83759 AN: 151916 Hom.: 25971 Cov.: 32 AF XY: 0.558 AC XY: 41426 AN XY: 74218

African (AFR) AF: 0.264 AC: 10970 AN: 41482

American (AMR) AF: 0.608 AC: 9250 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1779 AN: 3462

East Asian (EAS) AF: 0.379 AC: 1946 AN: 5134

South Asian (SAS) AF: 0.624 AC: 3002 AN: 4810

European-Finnish (FIN) AF: 0.772 AC: 8186 AN: 10604

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46789 AN: 67892

Other (OTH) AF: 0.547 AC: 1154 AN: 2110

Alfa AF: 0.647 Hom.: 54078

Bravo AF: 0.525

Asia WGS AF: 0.507 AC: 1762 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	1.8
DANN	Benign	0.61
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs10758939; hg19: chr9-8125410; COSMIC: COSV69445996;