5-5504729-C-T

Variant names:

• chr5-5504729-C-T
• rs2619855

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 0.542 in 151,924 control chromosomes in the GnomAD database, including 23,871 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 0.54 (23871 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.391
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.641 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: 0.542 AC: 82279 AN: 151806 Hom.: 23865 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.542 AC: 82302 AN: 151924 Hom.: 23871 Cov.: 32 AF XY: 0.541 AC XY: 40149 AN XY: 74266

African (AFR) AF: 0.334 AC: 13844 AN: 41412

American (AMR) AF: 0.627 AC: 9568 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2313 AN: 3470

East Asian (EAS) AF: 0.331 AC: 1709 AN: 5158

South Asian (SAS) AF: 0.630 AC: 3034 AN: 4816

European-Finnish (FIN) AF: 0.553 AC: 5826 AN: 10536

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43919 AN: 67940

Other (OTH) AF: 0.595 AC: 1258 AN: 2114

Alfa AF: 0.621 Hom.: 125539

Bravo AF: 0.539

Asia WGS AF: 0.487 AC: 1693 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.52
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs2619855; hg19: chr5-5504842;