Variant 15-38711562-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 variant allele was found at a frequency of 0.155 in 152,116 control chromosomes in the GnomAD database, including 2,355 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 0.16 ( 2355 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.213

Variant links:

Genes affected

(HGNC:):

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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.38711562C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect
LINC02694	ENST00000644461.1 linkuse as main transcript	n.96+83407C>T	intron_variant
LINC02694	ENST00000645416.2 linkuse as main transcript	n.52+8638C>T	intron_variant
LINC02694	ENST00000645994.1 linkuse as main transcript	n.142+14823C>T	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.155

AC:

23598

AN:

151998

Hom.:

2356

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0460

Gnomad AMI

AF:

0.170

Gnomad AMR

AF:

0.176

Gnomad ASJ

AF:

0.214

Gnomad EAS

AF:

0.0389

Gnomad SAS

AF:

0.0550

Gnomad FIN

AF:

0.219

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.219

Gnomad OTH

AF:

0.189

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

GnomAD4 genome

AF:

0.155

AC:

23587

AN:

152116

Hom.:

2355

Cov.:

AF XY:

0.153

AC XY:

11384

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.0459

Gnomad4 AMR

AF:

0.175

Gnomad4 ASJ

AF:

0.214

Gnomad4 EAS

AF:

0.0388

Gnomad4 SAS

AF:

0.0550

Gnomad4 FIN

AF:

0.219

Gnomad4 NFE

AF:

0.219

Gnomad4 OTH

AF:

0.188

Alfa

AF:

0.168

Hom.:

420

Bravo

AF:

0.150

Asia WGS

AF:

0.0770

AC:

268

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.5

DANN

Benign

0.40

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