chr4-54589777-C-T

Variant names:

• chr4-54589777-C-T
• rs17826780

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 0.108 in 152,116 control chromosomes in the GnomAD database, including 944 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 0.11 (944 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.867
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 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: 0.108 AC: 16480 AN: 151998 Hom.: 943 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.0275

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.108 AC: 16503 AN: 152116 Hom.: 944 Cov.: 32 AF XY: 0.109 AC XY: 8088 AN XY: 74380

African (AFR) AF: 0.116 AC: 4821 AN: 41496

American (AMR) AF: 0.0702 AC: 1073 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0775 AC: 269 AN: 3472

East Asian (EAS) AF: 0.0272 AC: 141 AN: 5186

South Asian (SAS) AF: 0.116 AC: 558 AN: 4812

European-Finnish (FIN) AF: 0.146 AC: 1540 AN: 10566

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7727 AN: 67988

Other (OTH) AF: 0.106 AC: 224 AN: 2110

Alfa AF: 0.111 Hom.: 485

Bravo AF: 0.102

Asia WGS AF: 0.0910 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.66
DANN	Benign	0.80
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs17826780; hg19: chr4-55455944;