Variant rs1441443 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_146637.1(LINC02005):n.348+4098A>C 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 0.32 in 152,072 control chromosomes in the GnomAD database, including 8,937 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 0.32 ( 8937 hom., cov: 32)

Consequence

LINC02005
NR_146637.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.970

Variant links:

Genes affected

LINC02005 (HGNC:52839): (long intergenic non-protein coding RNA 2005)

LINC02005 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=-0.66).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02005	NR_146637.1 linkuse as main transcript	n.348+4098A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
LINC02005	ENST00000498832.1 linkuse as main transcript	n.254+4098A>C	intron_variant, non_coding_transcript_variant	3
LINC02005	ENST00000659853.1 linkuse as main transcript	n.356+4098A>C	intron_variant, non_coding_transcript_variant
LINC02005	ENST00000664767.1 linkuse as main transcript	n.224+4098A>C	intron_variant, non_coding_transcript_variant
LINC02005	ENST00000670514.1 linkuse as main transcript	n.349+4098A>C	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.320

AC:

48596

AN:

151954

Hom.:

8935

Cov.:

show subpopulations

Gnomad AFR

AF:

0.420

Gnomad AMI

AF:

0.189

Gnomad AMR

AF:

0.407

Gnomad ASJ

AF:

0.280

Gnomad EAS

AF:

0.754

Gnomad SAS

AF:

0.244

Gnomad FIN

AF:

0.259

Gnomad MID

AF:

0.248

Gnomad NFE

AF:

0.226

Gnomad OTH

AF:

0.306

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

GnomAD4 genome

AF:

0.320

AC:

48635

AN:

152072

Hom.:

8937

Cov.:

AF XY:

0.327

AC XY:

24289

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.420

Gnomad4 AMR

AF:

0.407

Gnomad4 ASJ

AF:

0.280

Gnomad4 EAS

AF:

0.753

Gnomad4 SAS

AF:

0.244

Gnomad4 FIN

AF:

0.259

Gnomad4 NFE

AF:

0.226

Gnomad4 OTH

AF:

0.307

Alfa

AF:

0.249

Hom.:

9739

Bravo

AF:

0.343

Asia WGS

AF:

0.457

AC:

1589

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Benign

0.88

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