rs1358594

chr4-73689760-G-T

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 0.798 in 151,910 control chromosomes in the GnomAD database, including 51,439 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 0.80 (51439 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121253 AN: 151792 Hom.: 51434 Cov.: 31

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.813

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

GnomAD4 genome AF: 0.798 AC: 121277 AN: 151910 Hom.: 51439 Cov.: 31 AF XY: 0.800 AC XY: 59372 AN XY: 74248

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.894

Gnomad4 ASJ AF: 0.869

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.965

Gnomad4 NFE AF: 0.940

Gnomad4 OTH AF: 0.808

Alfa AF: 0.914 Hom.: 127279

Bravo AF: 0.780

Asia WGS AF: 0.723 AC: 2515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.72
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1358594; hg19: chr4-74555477;