Variant chr10-9286688-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000458168.1(LINC00709):n.125C>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 0.11 in 152,186 control chromosomes in the GnomAD database, including 1,045 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 0.11 ( 1045 hom., cov: 32)

Exomes 𝑓: 0.25 ( 0 hom. )

Consequence

LINC00709
ENST00000458168.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.501

Variant links:

Genes affected

LINC00709 (HGNC:44700): (long intergenic non-protein coding RNA 709)

LINC00709 links:

LOC101928272 (HGNC:):

LOC101928272 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=-0.85).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00709	NR_108039.1 link	n.345C>T		non_coding_transcript_exon_variant	2/2
LOC101928272	NR_120635.1 link	n.193-2299G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00709	ENST00000458168.1 link	n.125C>T		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16734

AN:

152064

Hom.:

1041

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.115

Gnomad AMR

AF:

0.204

Gnomad ASJ

AF:

0.0965

Gnomad EAS

AF:

0.0223

Gnomad SAS

AF:

0.0670

Gnomad FIN

AF:

0.111

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0927

Gnomad OTH

AF:

0.102

GnomAD4 exome

AF:

0.250

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

Gnomad4 NFE exome

AF:

0.250

GnomAD4 genome

AF:

0.110

AC:

16774

AN:

152182

Hom.:

1045

Cov.:

AF XY:

0.113

AC XY:

8445

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.122

Gnomad4 AMR

AF:

0.204

Gnomad4 ASJ

AF:

0.0965

Gnomad4 EAS

AF:

0.0224

Gnomad4 SAS

AF:

0.0689

Gnomad4 FIN

AF:

0.111

Gnomad4 NFE

AF:

0.0927

Gnomad4 OTH

AF:

0.101

Alfa

AF:

0.0809

Hom.:

350

Bravo

AF:

0.117

Asia WGS

AF:

0.0630

AC:

218

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.0

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