rs682585

Variant names:

• chr1-182590375-C-T
• rs682585

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 0.314 in 152,022 control chromosomes in the GnomAD database, including 8,789 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 0.31 (8789 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.436 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: 0.314 AC: 47750 AN: 151904 Hom.: 8789 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.314 AC: 47763 AN: 152022 Hom.: 8789 Cov.: 31 AF XY: 0.317 AC XY: 23514 AN XY: 74270

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.367

Alfa AF: 0.378 Hom.: 23009

Bravo AF: 0.311

Asia WGS AF: 0.329 AC: 1144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs682585; hg19: chr1-182559510;