Variant rs6017342 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000637248.1(LINC01620):n.330T>G 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 0.625 in 154,894 control chromosomes in the GnomAD database, including 31,089 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 0.63 ( 30579 hom., cov: 31)

Exomes 𝑓: 0.57 ( 510 hom. )

Consequence

LINC01620
ENST00000637248.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.639

Variant links:

Genes affected

LINC01620 (HGNC:):

LINC01620 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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.44436388A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01620	ENST00000637248.1 linkuse as main transcript	n.330T>G		non_coding_transcript_exon_variant	3/3	4

Frequencies

GnomAD3 genomes

AF:

0.625

AC:

94947

AN:

151834

Hom.:

30522

Cov.:

show subpopulations

Gnomad AFR

AF:

0.734

Gnomad AMI

AF:

0.656

Gnomad AMR

AF:

0.702

Gnomad ASJ

AF:

0.556

Gnomad EAS

AF:

0.892

Gnomad SAS

AF:

0.670

Gnomad FIN

AF:

0.554

Gnomad MID

AF:

0.661

Gnomad NFE

AF:

0.533

Gnomad OTH

AF:

0.631

GnomAD4 exome

AF:

0.572

AC:

1684

AN:

2942

Hom.:

510

Cov.:

AF XY:

0.571

AC XY:

925

AN XY:

1620

show subpopulations

Gnomad4 AFR exome

AF:

0.717

Gnomad4 AMR exome

AF:

0.720

Gnomad4 ASJ exome

AF:

0.583

Gnomad4 EAS exome

AF:

0.901

Gnomad4 SAS exome

AF:

0.679

Gnomad4 FIN exome

AF:

0.533

Gnomad4 NFE exome

AF:

0.526

Gnomad4 OTH exome

AF:

0.508

GnomAD4 genome

AF:

0.626

AC:

95057

AN:

151952

Hom.:

30579

Cov.:

AF XY:

0.629

AC XY:

46748

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.734

Gnomad4 AMR

AF:

0.703

Gnomad4 ASJ

AF:

0.556

Gnomad4 EAS

AF:

0.892

Gnomad4 SAS

AF:

0.670

Gnomad4 FIN

AF:

0.554

Gnomad4 NFE

AF:

0.533

Gnomad4 OTH

AF:

0.637

Alfa

AF:

0.562

Hom.:

44114

Bravo

AF:

0.643

Asia WGS

AF:

0.821

AC:

2853

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

1.3

DANN

Benign

0.39

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