rs2554380

Positions:

• chr15-83647132-C-T

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 0.851 in 152,254 control chromosomes in the GnomAD database, including 55,612 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 0.85 (55612 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.851 AC: 129453 AN: 152136 Hom.: 55562 Cov.: 33

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.851 AC: 129561 AN: 152254 Hom.: 55612 Cov.: 33 AF XY: 0.853 AC XY: 63505 AN XY: 74432

Gnomad4 AFR AF: 0.948

Gnomad4 AMR AF: 0.859

Gnomad4 ASJ AF: 0.886

Gnomad4 EAS AF: 0.962

Gnomad4 SAS AF: 0.928

Gnomad4 FIN AF: 0.762

Gnomad4 NFE AF: 0.789

Gnomad4 OTH AF: 0.841

Alfa AF: 0.806 Hom.: 102823

Bravo AF: 0.860

Asia WGS AF: 0.922 AC: 3208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0050
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2554380; hg19: chr15-84315884;