chr4-145954399-G-T

Variant names:

• chr4-145954399-G-T
• rs723794

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 0.633 in 151,998 control chromosomes in the GnomAD database, including 31,445 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 0.63 (31445 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.717 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: 0.633 AC: 96166 AN: 151880 Hom.: 31432 Cov.: 31

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.633 AC: 96217 AN: 151998 Hom.: 31445 Cov.: 31 AF XY: 0.629 AC XY: 46730 AN XY: 74288

African (AFR) AF: 0.485 AC: 20088 AN: 41430

American (AMR) AF: 0.682 AC: 10421 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1957 AN: 3468

East Asian (EAS) AF: 0.450 AC: 2321 AN: 5158

South Asian (SAS) AF: 0.555 AC: 2674 AN: 4816

European-Finnish (FIN) AF: 0.716 AC: 7566 AN: 10570

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.722 AC: 49092 AN: 67960

Other (OTH) AF: 0.608 AC: 1285 AN: 2112

Alfa AF: 0.676 Hom.: 67213

Bravo AF: 0.624

Asia WGS AF: 0.560 AC: 1946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.6
DANN	Benign	0.68
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs723794; hg19: chr4-146875551;