1-58584660-A-G

Variant names:

• chr1-58584660-A-G
• rs6690139

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 0.147 in 152,132 control chromosomes in the GnomAD database, including 1,699 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 0.15 (1699 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 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: 0.147 AC: 22274 AN: 152014 Hom.: 1698 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0523

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0934

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.147 AC: 22288 AN: 152132 Hom.: 1699 Cov.: 32 AF XY: 0.141 AC XY: 10463 AN XY: 74370

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.0522

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0934

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.139

Alfa AF: 0.146 Hom.: 856

Bravo AF: 0.148

Asia WGS AF: 0.0900 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.5
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6690139; hg19: chr1-59050332; COSMIC: COSV59945409;