chr5-173590084-C-T

Position:

• chr5-173590084-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;