18-51463692-C-A

Variant names:

• chr18-51463692-C-A
• rs321834
• ENST00000435144.7:n.219+71435C>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000435144.7(LINC01630):​n.219+71435C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0000073 (0 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC01630 ENST00000435144.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01630	NR_040074.1	n.216+71435C>A		intron_variant	Intron 1 of 2
LINC01630	NR_040075.1	n.217-1715C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01630	ENST00000435144.7	n.219+71435C>A		intron_variant	Intron 1 of 6	5
LINC01630	ENST00000578152.5	n.217-1715C>A		intron_variant	Intron 1 of 1	2
LINC01630	ENST00000580841.1	n.216+71435C>A		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.00000730 AC: 1 AN: 136928 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000231

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000730 AC: 1 AN: 137016 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 67004

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 36898

American (AMR) AF: 0.00 AC: 0 AN: 13884

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3256

East Asian (EAS) AF: 0.000231 AC: 1 AN: 4324

South Asian (SAS) AF: 0.00 AC: 0 AN: 3930

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9158

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 206

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 62628

Other (OTH) AF: 0.00 AC: 0 AN: 1914

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.47
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs321834; hg19: chr18-48990062;