rs321891

Variant names:

• chr18-51395516-C-T
• rs321891
• ENST00000435144.7:n.219+3259C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435144.7(LINC01630):​n.219+3259C>T variant causes a intron 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 ENST00000435144.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01630	NR_040074.1	n.216+3259C>T		intron_variant	Intron 1 of 2
LINC01630	NR_040075.1	n.216+3259C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01630	ENST00000435144.7	n.219+3259C>T		intron_variant	Intron 1 of 6	5
LINC01630	ENST00000578152.5	n.216+3259C>T		intron_variant	Intron 1 of 1	2
LINC01630	ENST00000580841.1	n.216+3259C>T		intron_variant	Intron 1 of 2	4

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

African (AFR) AF: 0.216 AC: 8971 AN: 41512

American (AMR) AF: 0.346 AC: 5294 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1309 AN: 3470

East Asian (EAS) AF: 0.341 AC: 1768 AN: 5182

South Asian (SAS) AF: 0.312 AC: 1501 AN: 4804

European-Finnish (FIN) AF: 0.325 AC: 3432 AN: 10548

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22667 AN: 67978

Other (OTH) AF: 0.308 AC: 650 AN: 2112

Alfa AF: 0.321 Hom.: 4429

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
PhyloP100		0.083

Splicing

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

Other links and lift over

dbSNP: rs321891; hg19: chr18-48921886;