chr4-56894258-G-T

Variant names:

• chr4-56894258-G-T
• rs4280803

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 0.0836 in 152,146 control chromosomes in the GnomAD database, including 819 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 0.084 (819 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.244
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0836 AC: 12702 AN: 152028 Hom.: 812 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.0184

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.0160

Gnomad FIN AF: 0.0708

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0427

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0836 AC: 12713 AN: 152146 Hom.: 819 Cov.: 32 AF XY: 0.0858 AC XY: 6383 AN XY: 74382

African (AFR) AF: 0.113 AC: 4687 AN: 41500

American (AMR) AF: 0.193 AC: 2938 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0184 AC: 64 AN: 3470

East Asian (EAS) AF: 0.218 AC: 1125 AN: 5154

South Asian (SAS) AF: 0.0156 AC: 75 AN: 4822

European-Finnish (FIN) AF: 0.0708 AC: 751 AN: 10612

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0427 AC: 2906 AN: 68008

Other (OTH) AF: 0.0753 AC: 159 AN: 2112

Alfa AF: 0.0676 Hom.: 65

Bravo AF: 0.0985

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.5
DANN	Benign	0.73
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs4280803; hg19: chr4-57760424;