dbSNP rs2150392: LINC00161:n.645C>A (chr21-28540130-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000412526.5(LINC00161):n.645C>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 0.501 in 151,922 control chromosomes in the GnomAD database, including 22,528 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 0.50 ( 22526 hom., cov: 31)

Exomes 𝑓: 0.83 ( 2 hom. )

Consequence

LINC00161
ENST00000412526.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.850

Variant links:

Genes affected

LINC00161 (HGNC:17138): (long intergenic non-protein coding RNA 161)

LINC00161 links:

ENSG00000232855 (HGNC:58104):

ENSG00000232855 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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00161	NR_026552.2 link	n.645C>A		non_coding_transcript_exon_variant	Exon 2 of 2
LINC00161	NR_026553.2 link	n.289C>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00161	ENST00000412526.5 link	n.645C>A	non_coding_transcript_exon_variant	Exon 2 of 2	2
LINC00161	ENST00000455939.1 link	n.289C>A	non_coding_transcript_exon_variant	Exon 2 of 2	2
ENSG00000232855	ENST00000430247.1 link	n.126+37145G>T	intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes

AF:

0.502

AC:

76133

AN:

151798

Hom.:

22530

Cov.:

show subpopulations

Gnomad AFR

AF:

0.208

Gnomad AMI

AF:

0.667

Gnomad AMR

AF:

0.487

Gnomad ASJ

AF:

0.591

Gnomad EAS

AF:

0.183

Gnomad SAS

AF:

0.474

Gnomad FIN

AF:

0.734

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.665

Gnomad OTH

AF:

0.543

GnomAD4 exome

AF:

0.833

AC:

AN:

Hom.:

Cov.:

AF XY:

0.833

AC XY:

AN XY:

show subpopulations

Gnomad4 NFE exome

AF:

0.833

GnomAD4 genome

AF:

0.501

AC:

76129

AN:

151916

Hom.:

22526

Cov.:

AF XY:

0.502

AC XY:

37282

AN XY:

74246

show subpopulations

Gnomad4 AFR

AF:

0.208

Gnomad4 AMR

AF:

0.486

Gnomad4 ASJ

AF:

0.591

Gnomad4 EAS

AF:

0.182

Gnomad4 SAS

AF:

0.476

Gnomad4 FIN

AF:

0.734

Gnomad4 NFE

AF:

0.665

Gnomad4 OTH

AF:

0.538

Alfa

AF:

0.597

Hom.:

13088

Bravo

AF:

0.469

Asia WGS

AF:

0.280

AC:

978

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.67

DANN

Benign

0.82

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