rs1701586

Variant names:

• chr18-63827393-G-A
• rs1701586

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.201 AC: 8342 AN: 41528

American (AMR) AF: 0.119 AC: 1821 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0807 AC: 280 AN: 3470

East Asian (EAS) AF: 0.429 AC: 2218 AN: 5174

South Asian (SAS) AF: 0.241 AC: 1156 AN: 4806

European-Finnish (FIN) AF: 0.0393 AC: 417 AN: 10606

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0719 AC: 4892 AN: 68010

Other (OTH) AF: 0.137 AC: 290 AN: 2114

Alfa AF: 0.102 Hom.: 195

Bravo AF: 0.139

Asia WGS AF: 0.349 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.68
DANN	Benign	0.33
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1701586; hg19: chr18-61494627;