10-27615267-T-G

Variant names:

• chr10-27615267-T-G
• rs1687730

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 0.833 in 152,130 control chromosomes in the GnomAD database, including 53,679 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 0.83 (53679 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.833 AC: 126600 AN: 152012 Hom.: 53652 Cov.: 33

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.833 AC: 126684 AN: 152130 Hom.: 53679 Cov.: 33 AF XY: 0.836 AC XY: 62190 AN XY: 74372

African (AFR) AF: 0.663 AC: 27478 AN: 41470

American (AMR) AF: 0.884 AC: 13518 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.902 AC: 3133 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5180 AN: 5186

South Asian (SAS) AF: 0.895 AC: 4318 AN: 4826

European-Finnish (FIN) AF: 0.908 AC: 9619 AN: 10592

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.891 AC: 60576 AN: 67988

Other (OTH) AF: 0.840 AC: 1770 AN: 2108

Alfa AF: 0.852 Hom.: 7234

Bravo AF: 0.824

Asia WGS AF: 0.924 AC: 3216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.42
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1687730; hg19: chr10-27904196;