15-27680690-C-T

Variant names:

• chr15-27680690-C-T
• rs737051

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 0.769 in 146,476 control chromosomes in the GnomAD database, including 44,611 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 0.77 (44611 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.566
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 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: 0.769 AC: 112532 AN: 146392 Hom.: 44561 Cov.: 26

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.769 AC: 112622 AN: 146476 Hom.: 44611 Cov.: 26 AF XY: 0.764 AC XY: 54677 AN XY: 71570

African (AFR) AF: 0.905 AC: 33208 AN: 36684

American (AMR) AF: 0.748 AC: 11219 AN: 15008

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2704 AN: 3468

East Asian (EAS) AF: 0.367 AC: 1876 AN: 5110

South Asian (SAS) AF: 0.591 AC: 2808 AN: 4754

European-Finnish (FIN) AF: 0.772 AC: 7993 AN: 10348

Middle Eastern (MID) AF: 0.755 AC: 216 AN: 286

European-Non Finnish (NFE) AF: 0.743 AC: 50383 AN: 67854

Other (OTH) AF: 0.734 AC: 1509 AN: 2056

Alfa AF: 0.763 Hom.: 65034

Bravo AF: 0.779

Asia WGS AF: 0.514 AC: 1785 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.2
DANN	Benign	0.38
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs737051; hg19: chr15-27925836;