Variant rs6695249 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_027379.1(LINC01555):n.227-350T>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 0.182 in 367,004 control chromosomes in the GnomAD database, including 6,801 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 0.19 ( 2851 hom., cov: 32)

Exomes 𝑓: 0.18 ( 3950 hom. )

Consequence

LINC01555
NR_027379.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0310

Variant links:

Genes affected

LINC01555 (HGNC:26647): (long intergenic non-protein coding RNA 1555)

LINC01555 links:

LOC124904206 (HGNC:):

LOC124904206 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=-1.02).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01555	NR_027379.1 linkuse as main transcript	n.227-350T>C		intron_variant, non_coding_transcript_variant
LOC124904206	XR_007066196.1 linkuse as main transcript	n.298-94A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01555	ENST00000370624.1 linkuse as main transcript	n.227-350T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.187

AC:

28411

AN:

152076

Hom.:

2834

Cov.:

show subpopulations

Gnomad AFR

AF:

0.244

Gnomad AMI

AF:

0.329

Gnomad AMR

AF:

0.228

Gnomad ASJ

AF:

0.219

Gnomad EAS

AF:

0.0593

Gnomad SAS

AF:

0.227

Gnomad FIN

AF:

0.121

Gnomad MID

AF:

0.276

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.197

GnomAD4 exome

AF:

0.178

AC:

38251

AN:

214806

Hom.:

3950

AF XY:

0.185

AC XY:

22188

AN XY:

120238

show subpopulations

Gnomad4 AFR exome

AF:

0.246

Gnomad4 AMR exome

AF:

0.257

Gnomad4 ASJ exome

AF:

0.217

Gnomad4 EAS exome

AF:

0.0559

Gnomad4 SAS exome

AF:

0.237

Gnomad4 FIN exome

AF:

0.129

Gnomad4 NFE exome

AF:

0.154

Gnomad4 OTH exome

AF:

0.174

GnomAD4 genome

AF:

0.187

AC:

28475

AN:

152198

Hom.:

2851

Cov.:

AF XY:

0.187

AC XY:

13887

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.245

Gnomad4 AMR

AF:

0.228

Gnomad4 ASJ

AF:

0.219

Gnomad4 EAS

AF:

0.0594

Gnomad4 SAS

AF:

0.228

Gnomad4 FIN

AF:

0.121

Gnomad4 NFE

AF:

0.156

Gnomad4 OTH

AF:

0.195

Alfa

AF:

0.171

Hom.:

3054

Bravo

AF:

0.196

Asia WGS

AF:

0.146

AC:

508

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.4

DANN

Benign

0.76

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