rs6716455

chr2-150269889-G-A

Variant summary

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

The ENST00000665690.1(LINC01818):n.200+55477G>A 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 0.117 in 152,198 control chromosomes in the GnomAD database, including 1,268 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 0.12 (1268 hom., cov: 33)
• Consequence: LINC01818 ENST00000665690.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500

Genes affected

LINC01818 (HGNC:52623): (long intergenic non-protein coding RNA 1818)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01818	XR_923469.3	n.249+55477G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01818	ENST00000665690.1	n.200+55477G>A		intron_variant, non_coding_transcript_variant
LINC01818	ENST00000437118.1	n.261-31084G>A		intron_variant, non_coding_transcript_variant		2
LINC01818	ENST00000659082.1	n.245+55477G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17765 AN: 152080 Hom.: 1268 Cov.: 33

Gnomad AFR AF: 0.0386

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.117 AC: 17765 AN: 152198 Hom.: 1268 Cov.: 33 AF XY: 0.118 AC XY: 8784 AN XY: 74380

Gnomad4 AFR AF: 0.0385

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.136

Alfa AF: 0.147 Hom.: 2671

Bravo AF: 0.113

Asia WGS AF: 0.146 AC: 508 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.96
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6716455; hg19: chr2-151126403;