rs1484556

Variant names:

• chr15-49749774-C-G
• rs1484556

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.252 in 152,008 control chromosomes in the GnomAD database, including 5,352 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 (5352 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.32 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: 0.253 AC: 38370 AN: 151890 Hom.: 5353 Cov.: 31

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.0744

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.252 AC: 38374 AN: 152008 Hom.: 5352 Cov.: 31 AF XY: 0.249 AC XY: 18478 AN XY: 74268

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.0746

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.279

Alfa AF: 0.278 Hom.: 767

Bravo AF: 0.246

Asia WGS AF: 0.130 AC: 452 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1484556; hg19: chr15-50041971;