dbSNP rs11156473: LINC01164:n.3250C>T (chr10-131772532-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000341866.3(LINC01164):n.3250C>T 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 0.13 in 152,352 control chromosomes in the GnomAD database, including 1,875 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 0.13 ( 1873 hom., cov: 33)

Exomes 𝑓: 0.12 ( 2 hom. )

Consequence

LINC01164
ENST00000341866.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.411

Variant links:

Genes affected

LINC01164 (HGNC:49533): (long intergenic non-protein coding RNA 1164)

LINC01164 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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01164	NR_038365.1 link	n.3250C>T		non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01164	ENST00000341866.3 link	n.3250C>T	non_coding_transcript_exon_variant	Exon 5 of 5	2
LINC01164	ENST00000655798.1 link	n.2650C>T	non_coding_transcript_exon_variant	Exon 6 of 6
LINC01164	ENST00000667493.1 link	n.3141C>T	non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.130

AC:

19760

AN:

152052

Hom.:

1873

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0309

Gnomad AMI

AF:

0.0691

Gnomad AMR

AF:

0.119

Gnomad ASJ

AF:

0.125

Gnomad EAS

AF:

0.449

Gnomad SAS

AF:

0.356

Gnomad FIN

AF:

0.145

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.151

Gnomad OTH

AF:

0.162

GnomAD4 exome

AF:

0.121

AC:

AN:

182

Hom.:

Cov.:

AF XY:

0.132

AC XY:

AN XY:

144

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.250

Gnomad4 FIN exome

AF:

0.313

Gnomad4 NFE exome

AF:

0.0956

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.130

AC:

19753

AN:

152170

Hom.:

1873

Cov.:

AF XY:

0.135

AC XY:

10010

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.0309

Gnomad4 AMR

AF:

0.119

Gnomad4 ASJ

AF:

0.125

Gnomad4 EAS

AF:

0.448

Gnomad4 SAS

AF:

0.356

Gnomad4 FIN

AF:

0.145

Gnomad4 NFE

AF:

0.150

Gnomad4 OTH

AF:

0.166

Alfa

AF:

0.131

Hom.:

201

Bravo

AF:

0.121

Asia WGS

AF:

0.365

AC:

1266

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.7

DANN

Benign

0.74

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