5-52578147-C-T

Variant names:

• chr5-52578147-C-T
• rs1600172

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 0.882 in 152,138 control chromosomes in the GnomAD database, including 59,311 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 0.88 (59311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.882 AC: 134074 AN: 152020 Hom.: 59258 Cov.: 32

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.882 AC: 134185 AN: 152138 Hom.: 59311 Cov.: 32 AF XY: 0.881 AC XY: 65507 AN XY: 74372

African (AFR) AF: 0.908 AC: 37713 AN: 41524

American (AMR) AF: 0.846 AC: 12904 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3102 AN: 3470

East Asian (EAS) AF: 0.684 AC: 3522 AN: 5146

South Asian (SAS) AF: 0.838 AC: 4051 AN: 4832

European-Finnish (FIN) AF: 0.910 AC: 9653 AN: 10602

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.887 AC: 60339 AN: 67996

Other (OTH) AF: 0.872 AC: 1839 AN: 2110

Alfa AF: 0.888 Hom.: 7298

Bravo AF: 0.878

Asia WGS AF: 0.784 AC: 2728 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.4
DANN	Benign	0.53
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs1600172; hg19: chr5-51873981; COSMIC: COSV72818571;