5-1450329-C-T

Variant names:

• chr5-1450329-C-T
• rs2550948

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 151,860 control chromosomes in the GnomAD database, including 18,079 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 (18079 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 20 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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: 69864 AN: 151742 Hom.: 18069 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.591

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: 69908 AN: 151860 Hom.: 18079 Cov.: 32 AF XY: 0.460 AC XY: 34109 AN XY: 74206

African (AFR) AF: 0.237 AC: 9834 AN: 41416

American (AMR) AF: 0.464 AC: 7077 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2058 AN: 3470

East Asian (EAS) AF: 0.162 AC: 838 AN: 5172

South Asian (SAS) AF: 0.476 AC: 2287 AN: 4804

European-Finnish (FIN) AF: 0.560 AC: 5874 AN: 10486

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

European-Non Finnish (NFE) AF: 0.591 AC: 40175 AN: 67938

Other (OTH) AF: 0.497 AC: 1048 AN: 2110

Alfa AF: 0.545 Hom.: 40649

Bravo AF: 0.439

Asia WGS AF: 0.335 AC: 1165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.35
DANN	Benign	0.75
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2550948; hg19: chr5-1450444;