rs7581641

chr2-8485976-C-T

Variant summary

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

The ENST00000670008.1(LINC01814):n.1018-23580G>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 0.101 in 152,208 control chromosomes in the GnomAD database, including 1,692 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 0.10 (1692 hom., cov: 32)
• Consequence: LINC01814 ENST00000670008.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.61

Genes affected

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

LINC00299 (HGNC:27940): (long intergenic non-protein coding RNA 299)

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 (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01814	ENST00000670008.1	n.1018-23580G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15363 AN: 152090 Hom.: 1683 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0586

Gnomad ASJ AF: 0.0458

Gnomad EAS AF: 0.0449

Gnomad SAS AF: 0.0928

Gnomad FIN AF: 0.0268

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0270

Gnomad OTH AF: 0.0934

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

GnomAD4 genome AF: 0.101 AC: 15412 AN: 152208 Hom.: 1692 Cov.: 32 AF XY: 0.101 AC XY: 7547 AN XY: 74428

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.0586

Gnomad4 ASJ AF: 0.0458

Gnomad4 EAS AF: 0.0448

Gnomad4 SAS AF: 0.0923

Gnomad4 FIN AF: 0.0268

Gnomad4 NFE AF: 0.0270

Gnomad4 OTH AF: 0.0986

Alfa AF: 0.0510 Hom.: 254

Bravo AF: 0.109

Asia WGS AF: 0.109 AC: 381 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	0.038
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7581641; hg19: chr2-8626106;