rs723794

Variant names:

• chr4-145954399-G-T
• rs723794

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.608

Alfa AF: 0.694 Hom.: 48640

Bravo AF: 0.624

Asia WGS AF: 0.560 AC: 1946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs723794; hg19: chr4-146875551;