rs2554380

Variant names:

• chr15-83647132-C-T
• rs2554380

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 0.851 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
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.948 AC: 39389 AN: 41560

American (AMR) AF: 0.859 AC: 13127 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.886 AC: 3076 AN: 3472

East Asian (EAS) AF: 0.962 AC: 4987 AN: 5186

South Asian (SAS) AF: 0.928 AC: 4475 AN: 4824

European-Finnish (FIN) AF: 0.762 AC: 8065 AN: 10580

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.789 AC: 53659 AN: 68022

Other (OTH) AF: 0.841 AC: 1780 AN: 2116

Alfa AF: 0.814 Hom.: 212118

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2554380; hg19: chr15-84315884;