rs1978503

chr18-55997051-A-G

Variant summary

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

The ENST00000654280.1(LINC01416):n.1169T>C 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 0.181 in 152,112 control chromosomes in the GnomAD database, including 2,580 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 0.18 (2580 hom., cov: 32)
• Consequence: LINC01416 ENST00000654280.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381

Genes affected

LINC01416 (HGNC:51645): (long intergenic non-protein coding RNA 1416)

LINC03092 (HGNC:56721): (long intergenic non-protein coding RNA 3092)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03092	XR_001753454.2	n.841A>G		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01416	ENST00000654280.1	n.1169T>C		non_coding_transcript_exon_variant	1/4
LINC03092	ENST00000589440.1	n.406-20677A>G		intron_variant, non_coding_transcript_variant		2
LINC01416	ENST00000655696.1	n.960T>C		non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27507 AN: 151994 Hom.: 2572 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.181 AC: 27546 AN: 152112 Hom.: 2580 Cov.: 32 AF XY: 0.178 AC XY: 13201 AN XY: 74364

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.183

Alfa AF: 0.189 Hom.: 6435

Bravo AF: 0.181

Asia WGS AF: 0.158 AC: 549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.8
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1978503; hg19: chr18-53664282; COSMIC: COSV74054574;