rs2550946

Variant names:

• chr5-1450398-A-G
• rs2550946

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 0.46 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.238 AC: 9867 AN: 41412

American (AMR) AF: 0.463 AC: 7067 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2055 AN: 3468

East Asian (EAS) AF: 0.163 AC: 840 AN: 5150

South Asian (SAS) AF: 0.477 AC: 2290 AN: 4802

European-Finnish (FIN) AF: 0.556 AC: 5815 AN: 10460

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40111 AN: 67800

Other (OTH) AF: 0.496 AC: 1046 AN: 2108

Alfa AF: 0.497 Hom.: 7085

Bravo AF: 0.441

Asia WGS AF: 0.336 AC: 1169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.29
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs2550946; hg19: chr5-1450513;