2-8527521-C-T

Position:

• chr2-8527521-C-T

Variant summary

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

The ENST00000670008.1(LINC01814):​n.1017+49390G>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 0.624 in 151,944 control chromosomes in the GnomAD database, including 31,443 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 0.62 (31443 hom., cov: 31)
• Consequence: LINC01814 ENST00000670008.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.628

Genes affected

LINC01814 (HGNC:52618): (long intergenic non-protein coding RNA 1814)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01814	ENST00000670008.1	n.1017+49390G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94776 AN: 151826 Hom.: 31443 Cov.: 31

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.624 AC: 94789 AN: 151944 Hom.: 31443 Cov.: 31 AF XY: 0.629 AC XY: 46691 AN XY: 74256

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.748

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.790

Gnomad4 FIN AF: 0.763

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.640

Alfa AF: 0.656 Hom.: 6320

Bravo AF: 0.609

Asia WGS AF: 0.664 AC: 2309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.7
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12624227; hg19: chr2-8667651;