chr10-12272998-A-G

Variant names:

• chr10-12272998-A-G
• rs10906115

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 0.374 in 151,934 control chromosomes in the GnomAD database, including 10,992 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 0.37 (10992 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518
• Publications: 86 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.463 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: 0.374 AC: 56772 AN: 151816 Hom.: 10980 Cov.: 31

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.374 AC: 56822 AN: 151934 Hom.: 10992 Cov.: 31 AF XY: 0.378 AC XY: 28027 AN XY: 74240

African (AFR) AF: 0.310 AC: 12837 AN: 41440

American (AMR) AF: 0.445 AC: 6771 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1315 AN: 3472

East Asian (EAS) AF: 0.406 AC: 2090 AN: 5154

South Asian (SAS) AF: 0.479 AC: 2311 AN: 4820

European-Finnish (FIN) AF: 0.348 AC: 3668 AN: 10544

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.392 AC: 26654 AN: 67978

Other (OTH) AF: 0.378 AC: 796 AN: 2106

Alfa AF: 0.388 Hom.: 55405

Bravo AF: 0.370

Asia WGS AF: 0.471 AC: 1643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.43
DANN	Benign	0.34
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs10906115; hg19: chr10-12314997;