Variant rs17529983 details in Genebe, Genetics Data Aggregator

Variant summary

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

The XR_950141.1(LINC02705):n.4084C>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 0.306 in 151,348 control chromosomes in the GnomAD database, including 8,646 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 0.31 ( 8643 hom., cov: 31)

Exomes 𝑓: 0.35 ( 3 hom. )

Consequence

LINC02705
XR_950141.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.64

Variant links:

Genes affected

LINC02705 (HGNC:):

LINC02705 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=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
LINC02705	XR_950141.1 linkuse as main transcript	n.4084C>T	non_coding_transcript_exon_variant	3/3
LINC02705	XR_950142.1 linkuse as main transcript	n.3597C>T	non_coding_transcript_exon_variant	4/4
	use as main transcript	n.60159566G>A	intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.306

AC:

46251

AN:

151208

Hom.:

8645

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0971

Gnomad AMI

AF:

0.426

Gnomad AMR

AF:

0.300

Gnomad ASJ

AF:

0.382

Gnomad EAS

AF:

0.208

Gnomad SAS

AF:

0.515

Gnomad FIN

AF:

0.310

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.418

Gnomad OTH

AF:

0.359

GnomAD4 exome

AF:

0.346

AC:

AN:

Hom.:

AF XY:

0.350

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 SAS exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.389

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.306

AC:

46248

AN:

151322

Hom.:

8643

Cov.:

AF XY:

0.305

AC XY:

22549

AN XY:

73866

show subpopulations

Gnomad4 AFR

AF:

0.0970

Gnomad4 AMR

AF:

0.299

Gnomad4 ASJ

AF:

0.382

Gnomad4 EAS

AF:

0.207

Gnomad4 SAS

AF:

0.515

Gnomad4 FIN

AF:

0.310

Gnomad4 NFE

AF:

0.418

Gnomad4 OTH

AF:

0.360

Alfa

AF:

0.338

Hom.:

1216

Bravo

AF:

0.290

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.4

DANN

Benign

0.48

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