chr15-74727909-C-A

Variant names:

• chr15-74727909-C-A
• rs17861109

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 0.22 in 152,054 control chromosomes in the GnomAD database, including 5,022 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 0.22 (5022 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 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: 0.219 AC: 33330 AN: 151936 Hom.: 4996 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.220 AC: 33418 AN: 152054 Hom.: 5022 Cov.: 32 AF XY: 0.226 AC XY: 16790 AN XY: 74348

African (AFR) AF: 0.362 AC: 14994 AN: 41428

American (AMR) AF: 0.352 AC: 5387 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 434 AN: 3472

East Asian (EAS) AF: 0.409 AC: 2103 AN: 5146

South Asian (SAS) AF: 0.325 AC: 1565 AN: 4810

European-Finnish (FIN) AF: 0.128 AC: 1353 AN: 10602

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6946 AN: 67980

Other (OTH) AF: 0.221 AC: 468 AN: 2116

Alfa AF: 0.0512 Hom.: 54

Bravo AF: 0.240

Asia WGS AF: 0.423 AC: 1467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.85
DANN	Benign	0.49
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs17861109; hg19: chr15-75020250;