rs7612209

chr3-177879201-G-Achr3-177879201-G-C

Variant summary

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

The NR_110826.1(LINC02015):n.133-16412G>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 0.51 in 152,082 control chromosomes in the GnomAD database, including 22,323 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 0.51 (22323 hom., cov: 32)
• Consequence: LINC02015 NR_110826.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

LINC02015 (HGNC:52850): (long intergenic non-protein coding RNA 2015)

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 = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02015	NR_110826.1	n.133-16412G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02015	ENST00000436078.5	n.133-16412G>A		intron_variant, non_coding_transcript_variant		2
LINC02015	ENST00000434309.2	n.49-16412G>A		intron_variant, non_coding_transcript_variant		4
LINC02015	ENST00000654164.1	n.125-16412G>A		intron_variant, non_coding_transcript_variant
LINC02015	ENST00000668196.1	n.242-16412G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77582 AN: 151964 Hom.: 22324 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.510 AC: 77589 AN: 152082 Hom.: 22323 Cov.: 32 AF XY: 0.510 AC XY: 37881 AN XY: 74336

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.553

Alfa AF: 0.619 Hom.: 43761

Bravo AF: 0.494

Asia WGS AF: 0.421 AC: 1465 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	1.4
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7612209; hg19: chr3-177596989;