5-52575488-C-T

Variant names:

• chr5-52575488-C-T
• rs10461556

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 0.349 in 151,864 control chromosomes in the GnomAD database, including 10,901 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 0.35 (10901 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53058 AN: 151746 Hom.: 10904 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.426

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.349 AC: 53057 AN: 151864 Hom.: 10901 Cov.: 32 AF XY: 0.349 AC XY: 25924 AN XY: 74196

African (AFR) AF: 0.129 AC: 5371 AN: 41484

American (AMR) AF: 0.348 AC: 5291 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1869 AN: 3468

East Asian (EAS) AF: 0.326 AC: 1672 AN: 5128

South Asian (SAS) AF: 0.303 AC: 1460 AN: 4824

European-Finnish (FIN) AF: 0.477 AC: 5036 AN: 10556

Middle Eastern (MID) AF: 0.421 AC: 122 AN: 290

European-Non Finnish (NFE) AF: 0.456 AC: 30955 AN: 67880

Other (OTH) AF: 0.373 AC: 786 AN: 2106

Alfa AF: 0.419 Hom.: 7140

Bravo AF: 0.333

Asia WGS AF: 0.292 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs10461556; hg19: chr5-51871322;