Variant rs1407379 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_121585.1(LINC01231):n.619C>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 0.229 in 152,114 control chromosomes in the GnomAD database, including 4,711 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 0.23 ( 4711 hom., cov: 33)

Failed GnomAD Quality Control

Consequence

LINC01231
NR_121585.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0110

Variant links:

Genes affected

LINC01231 (HGNC:49688): (long intergenic non-protein coding RNA 1231)

LINC01231 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01231	NR_121585.1 linkuse as main transcript	n.619C>A		non_coding_transcript_exon_variant	4/5

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
LINC01231	ENST00000663825.1 linkuse as main transcript	n.748C>A	non_coding_transcript_exon_variant	3/3
LINC01231	ENST00000452746.1 linkuse as main transcript	n.619C>A	non_coding_transcript_exon_variant	4/4	3
LINC01231	ENST00000654614.1 linkuse as main transcript	n.426C>A	non_coding_transcript_exon_variant	3/4
LINC01231	ENST00000659476.1 linkuse as main transcript	n.1050+8C>A	splice_region_variant, intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.229

AC:

34774

AN:

151996

Hom.:

4706

Cov.:

show subpopulations

Gnomad AFR

AF:

0.336

Gnomad AMI

AF:

0.236

Gnomad AMR

AF:

0.265

Gnomad ASJ

AF:

0.206

Gnomad EAS

AF:

0.477

Gnomad SAS

AF:

0.207

Gnomad FIN

AF:

0.169

Gnomad MID

AF:

0.309

Gnomad NFE

AF:

0.147

Gnomad OTH

AF:

0.248

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

GnomAD4 genome

AF:

0.229

AC:

34798

AN:

152114

Hom.:

4711

Cov.:

AF XY:

0.232

AC XY:

17221

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.336

Gnomad4 AMR

AF:

0.265

Gnomad4 ASJ

AF:

0.206

Gnomad4 EAS

AF:

0.477

Gnomad4 SAS

AF:

0.206

Gnomad4 FIN

AF:

0.169

Gnomad4 NFE

AF:

0.147

Gnomad4 OTH

AF:

0.250

Alfa

AF:

0.175

Hom.:

1291

Bravo

AF:

0.246

Asia WGS

AF:

0.308

AC:

1070

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.90

DANN

Benign

0.45

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