chr10-18139055-G-A

Variant names:

• chr10-18139055-G-A
• rs7909119

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 0.303 in 151,444 control chromosomes in the GnomAD database, including 7,229 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 0.30 (7229 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.364 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: 0.303 AC: 45880 AN: 151324 Hom.: 7208 Cov.: 31

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.303 AC: 45927 AN: 151444 Hom.: 7229 Cov.: 31 AF XY: 0.305 AC XY: 22565 AN XY: 74010

African (AFR) AF: 0.364 AC: 15035 AN: 41278

American (AMR) AF: 0.372 AC: 5672 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 798 AN: 3468

East Asian (EAS) AF: 0.218 AC: 1106 AN: 5064

South Asian (SAS) AF: 0.268 AC: 1281 AN: 4788

European-Finnish (FIN) AF: 0.277 AC: 2914 AN: 10530

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.269 AC: 18206 AN: 67774

Other (OTH) AF: 0.289 AC: 608 AN: 2102

Alfa AF: 0.294 Hom.: 847

Bravo AF: 0.312

Asia WGS AF: 0.240 AC: 835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.2
DANN	Benign	0.87
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs7909119; hg19: chr10-18427984;