5-172542345-C-T

Position:

• chr5-172542345-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 0.1 in 152,064 control chromosomes in the GnomAD database, including 834 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 0.10 (834 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15209 AN: 151946 Hom.: 834 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.0810

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0284

Gnomad SAS AF: 0.0786

Gnomad FIN AF: 0.0896

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0778

Gnomad OTH AF: 0.0908

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

GnomAD4 genome AF: 0.100 AC: 15227 AN: 152064 Hom.: 834 Cov.: 32 AF XY: 0.0998 AC XY: 7419 AN XY: 74322

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.0809

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.0284

Gnomad4 SAS AF: 0.0797

Gnomad4 FIN AF: 0.0896

Gnomad4 NFE AF: 0.0778

Gnomad4 OTH AF: 0.0908

Alfa AF: 0.0751 Hom.: 321

Bravo AF: 0.101

Asia WGS AF: 0.0740 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1347155; hg19: chr5-171969348;