rs188918

Variant names:

• chr18-51641379-A-G
• rs188918
• ENST00000635103.1:n.1732A>G

Your query was ambiguous. Multiple possible variants found:

• chr18-51641379-A-G
• chr18-51641379-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635103.1(LINC01630):​n.1732A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 151,952 control chromosomes in the GnomAD database, including 36,127 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 0.68 (36127 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC01630 ENST00000635103.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825

Genes affected

LINC01630 (HGNC:52295): (long intergenic non-protein coding RNA 1630)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 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
LINC01630	ENST00000635103.1	n.1732A>G		non_coding_transcript_exon_variant	Exon 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103586 AN: 151834 Hom.: 36110 Cov.: 32

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.657

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.682 AC: 103652 AN: 151952 Hom.: 36127 Cov.: 32 AF XY: 0.683 AC XY: 50729 AN XY: 74226

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.655

Alfa AF: 0.649 Hom.: 5500

Bravo AF: 0.695

Asia WGS AF: 0.818 AC: 2843 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
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: rs188918; hg19: chr18-49167749;