chr5-172542345-C-T

Variant names:

• chr5-172542345-C-T
• rs1347155

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;