chr4-52237726-T-C

Variant names:

• chr4-52237726-T-C
• rs4470701

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 0.527 in 151,778 control chromosomes in the GnomAD database, including 24,560 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 0.53 (24560 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.683 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: 0.527 AC: 79970 AN: 151662 Hom.: 24571 Cov.: 29

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.527 AC: 79980 AN: 151778 Hom.: 24560 Cov.: 29 AF XY: 0.528 AC XY: 39187 AN XY: 74166

African (AFR) AF: 0.192 AC: 7940 AN: 41370

American (AMR) AF: 0.536 AC: 8168 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2381 AN: 3466

East Asian (EAS) AF: 0.512 AC: 2630 AN: 5134

South Asian (SAS) AF: 0.616 AC: 2963 AN: 4812

European-Finnish (FIN) AF: 0.677 AC: 7130 AN: 10536

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46715 AN: 67918

Other (OTH) AF: 0.578 AC: 1219 AN: 2110

Alfa AF: 0.627 Hom.: 50415

Bravo AF: 0.505

Asia WGS AF: 0.537 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.48
PhyloP100		0.025

Splicing

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

Other links and lift over

dbSNP: rs4470701; hg19: chr4-53103892;