rs2550946

Variant names:

• chr5-1450398-A-G
• rs2550946

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 0.46 in 151,652 control chromosomes in the GnomAD database, including 18,010 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 0.46 (18010 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.821

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.587 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: 0.460 AC: 69760 AN: 151534 Hom.: 18001 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.460 AC: 69802 AN: 151652 Hom.: 18010 Cov.: 32 AF XY: 0.459 AC XY: 34001 AN XY: 74054

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.496

Alfa AF: 0.507 Hom.: 3893

Bravo AF: 0.441

Asia WGS AF: 0.336 AC: 1169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2550946; hg19: chr5-1450513;