15-78559273-G-A

Variant names:

• chr15-78559273-G-A
• rs2036527

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 0.288 in 152,096 control chromosomes in the GnomAD database, including 6,845 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 0.29 (6845 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762
• Publications: 122 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.346 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: 0.288 AC: 43709 AN: 151978 Hom.: 6838 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.0340

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.288 AC: 43744 AN: 152096 Hom.: 6845 Cov.: 33 AF XY: 0.284 AC XY: 21105 AN XY: 74348

African (AFR) AF: 0.221 AC: 9187 AN: 41478

American (AMR) AF: 0.240 AC: 3673 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1233 AN: 3470

East Asian (EAS) AF: 0.0343 AC: 178 AN: 5194

South Asian (SAS) AF: 0.225 AC: 1087 AN: 4828

European-Finnish (FIN) AF: 0.329 AC: 3474 AN: 10560

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23776 AN: 67964

Other (OTH) AF: 0.306 AC: 645 AN: 2110

Alfa AF: 0.322 Hom.: 33126

Bravo AF: 0.277

Asia WGS AF: 0.134 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.47
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs2036527; hg19: chr15-78851615;