5-173590084-C-T

Variant names:

• chr5-173590084-C-T
• rs1363605

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 0.25 in 152,108 control chromosomes in the GnomAD database, including 6,025 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 0.25 (6025 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 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: 0.250 AC: 38038 AN: 151990 Hom.: 6012 Cov.: 33

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.250 AC: 38081 AN: 152108 Hom.: 6025 Cov.: 33 AF XY: 0.251 AC XY: 18679 AN XY: 74360

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.250

Alfa AF: 0.185 Hom.: 1501

Bravo AF: 0.263

Asia WGS AF: 0.447 AC: 1552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.9
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1363605; hg19: chr5-173017087;