chr1-58599895-A-T

Position:

• chr1-58599895-A-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 0.472 in 150,930 control chromosomes in the GnomAD database, including 17,955 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 0.47 (17955 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 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: 0.472 AC: 71216 AN: 150818 Hom.: 17935 Cov.: 30

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.472 AC: 71278 AN: 150930 Hom.: 17955 Cov.: 30 AF XY: 0.476 AC XY: 35037 AN XY: 73662

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.429

Alfa AF: 0.285 Hom.: 703

Bravo AF: 0.478

Asia WGS AF: 0.538 AC: 1864 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.5
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs107399; hg19: chr1-59065567;