5-172542345-C-T

Variant names:

• chr5-172542345-C-T
• rs1347155

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 0.1 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.159 AC: 6588 AN: 41432

American (AMR) AF: 0.0809 AC: 1236 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 363 AN: 3470

East Asian (EAS) AF: 0.0284 AC: 147 AN: 5172

South Asian (SAS) AF: 0.0797 AC: 384 AN: 4816

European-Finnish (FIN) AF: 0.0896 AC: 948 AN: 10576

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0778 AC: 5294 AN: 68006

Other (OTH) AF: 0.0908 AC: 191 AN: 2104

Alfa AF: 0.0769 Hom.: 395

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
PhyloP100		0.017

Splicing

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

Other links and lift over

dbSNP: rs1347155; hg19: chr5-171969348;