chr15-49711886-T-C

Variant names:

• chr15-49711886-T-C
• rs17404727

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 0.255 in 152,240 control chromosomes in the GnomAD database, including 5,954 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 0.25 (5954 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.815
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38791 AN: 152122 Hom.: 5954 Cov.: 33

Gnomad AFR AF: 0.0858

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.255 AC: 38775 AN: 152240 Hom.: 5954 Cov.: 33 AF XY: 0.251 AC XY: 18716 AN XY: 74428

African (AFR) AF: 0.0856 AC: 3559 AN: 41556

American (AMR) AF: 0.252 AC: 3848 AN: 15294

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

East Asian (EAS) AF: 0.192 AC: 993 AN: 5182

South Asian (SAS) AF: 0.207 AC: 997 AN: 4824

European-Finnish (FIN) AF: 0.283 AC: 2996 AN: 10602

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24044 AN: 67992

Other (OTH) AF: 0.271 AC: 574 AN: 2116

Alfa AF: 0.311 Hom.: 2778

Asia WGS AF: 0.183 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.0
DANN	Benign	0.58
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs17404727; hg19: chr15-50004083;