chr15-38720378-C-T

Variant summary

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

The ENST00000644461.1(LINC02694):​n.96+92223C>T 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 0.311 in 152,120 control chromosomes in the GnomAD database, including 7,797 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 ( 7797 hom., cov: 33)

Consequence

LINC02694
ENST00000644461.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0470
Variant links:
Genes affected
LINC02694 (HGNC:33796): (long intergenic non-protein coding RNA 2694)

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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 (EAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LINC02694ENST00000644461.1 linkuse as main transcriptn.96+92223C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.312
AC:
47351
AN:
152004
Hom.:
7810
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.223
Gnomad AMI
AF:
0.541
Gnomad AMR
AF:
0.372
Gnomad ASJ
AF:
0.317
Gnomad EAS
AF:
0.563
Gnomad SAS
AF:
0.487
Gnomad FIN
AF:
0.286
Gnomad MID
AF:
0.342
Gnomad NFE
AF:
0.320
Gnomad OTH
AF:
0.329
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.311
AC:
47355
AN:
152120
Hom.:
7797
Cov.:
33
AF XY:
0.316
AC XY:
23490
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.223
Gnomad4 AMR
AF:
0.372
Gnomad4 ASJ
AF:
0.317
Gnomad4 EAS
AF:
0.562
Gnomad4 SAS
AF:
0.486
Gnomad4 FIN
AF:
0.286
Gnomad4 NFE
AF:
0.320
Gnomad4 OTH
AF:
0.326
Alfa
AF:
0.321
Hom.:
16354
Bravo
AF:
0.311
Asia WGS
AF:
0.444
AC:
1543
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.7
DANN
Benign
0.64

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.

Other links and lift over

dbSNP: rs8024474; hg19: chr15-39012579; API