rs1701586

Variant names:

• chr18-63827393-G-A
• rs1701586

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 0.128 in 152,198 control chromosomes in the GnomAD database, including 1,842 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 0.13 (1842 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 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: 0.128 AC: 19447 AN: 152080 Hom.: 1840 Cov.: 33

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.0393

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0719

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.128 AC: 19469 AN: 152198 Hom.: 1842 Cov.: 33 AF XY: 0.130 AC XY: 9689 AN XY: 74402

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.0807

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.0393

Gnomad4 NFE AF: 0.0719

Gnomad4 OTH AF: 0.137

Alfa AF: 0.0998 Hom.: 184

Bravo AF: 0.139

Asia WGS AF: 0.349 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.68
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1701586; hg19: chr18-61494627;