dbSNP rs1048828: LINC00867:n.720T>A (chr10-118365003-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000415417.6(LINC00867):n.720T>A 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 0.427 in 152,094 control chromosomes in the GnomAD database, including 15,688 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 0.43 ( 15686 hom., cov: 32)

Exomes 𝑓: 0.43 ( 2 hom. )

Consequence

LINC00867
ENST00000415417.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.189

Variant links:

Genes affected

LINC00867 (HGNC:45265): (long intergenic non-protein coding RNA 867)

LINC00867 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00867	ENST00000415417.6 link	n.720T>A	non_coding_transcript_exon_variant	Exon 4 of 4	3
LINC00867	ENST00000453236.2 link	n.921T>A	non_coding_transcript_exon_variant	Exon 3 of 3	3
LINC00867	ENST00000657224.1 link	n.707T>A	non_coding_transcript_exon_variant	Exon 2 of 2
LINC00867	ENST00000668223.1 link	n.469+7155T>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.428

AC:

65020

AN:

151960

Hom.:

15697

Cov.:

show subpopulations

Gnomad AFR

AF:

0.194

Gnomad AMI

AF:

0.461

Gnomad AMR

AF:

0.366

Gnomad ASJ

AF:

0.503

Gnomad EAS

AF:

0.480

Gnomad SAS

AF:

0.525

Gnomad FIN

AF:

0.639

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.536

Gnomad OTH

AF:

0.423

GnomAD4 exome

AF:

0.429

AC:

AN:

Hom.:

Cov.:

AF XY:

0.417

AC XY:

AN XY:

show subpopulations

Gnomad4 AMR exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.500

GnomAD4 genome

AF:

0.427

AC:

65010

AN:

152080

Hom.:

15686

Cov.:

AF XY:

0.433

AC XY:

32213

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.194

Gnomad4 AMR

AF:

0.365

Gnomad4 ASJ

AF:

0.503

Gnomad4 EAS

AF:

0.480

Gnomad4 SAS

AF:

0.525

Gnomad4 FIN

AF:

0.639

Gnomad4 NFE

AF:

0.536

Gnomad4 OTH

AF:

0.418

Alfa

AF:

0.483

Hom.:

2353

Bravo

AF:

0.392

Asia WGS

AF:

0.430

AC:

1496

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

DANN

Benign

0.65

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over