rs321891

Positions:

• chr18-51395516-C-T

Variant summary

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

The NR_040074.1(LINC01630):​n.216+3259C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,104 control chromosomes in the GnomAD database, including 7,209 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 0.30 (7209 hom., cov: 32)
• Consequence: LINC01630 NR_040074.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01630	NR_040074.1	n.216+3259C>T		intron_variant, non_coding_transcript_variant
LINC01630	NR_040075.1	n.216+3259C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01630	ENST00000635680.1	n.260+3259C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46040 AN: 151986 Hom.: 7207 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.303 AC: 46057 AN: 152104 Hom.: 7209 Cov.: 32 AF XY: 0.303 AC XY: 22513 AN XY: 74336

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.308

Alfa AF: 0.320 Hom.: 3976

Bravo AF: 0.302

Asia WGS AF: 0.283 AC: 982 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	3.3
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: rs321891; hg19: chr18-48921886;