rs726657

Variant summary

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

The ENST00000648852.1(DELEC1):​n.198+12458C>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 0.495 in 152,084 control chromosomes in the GnomAD database, including 19,778 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 0.50 ( 19778 hom., cov: 32)

Consequence

DELEC1
ENST00000648852.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.386
Variant links:
Genes affected
DELEC1 (HGNC:23658): (deleted in esophageal cancer 1) The function of this gene is not known. This gene is located in a region commonly deleted in esophageal squamous cell carcinomas. Gene expression is reduced or absent in these carcinomas and thus this is a candidate tumor suppressor gene for esophageal squamous cell carcinomas. [provided by RefSeq, Jul 2008]

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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 (AFR) allele frequency at 95% confidence interval = 0.667 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
DELEC1ENST00000648852.1 linkuse as main transcriptn.198+12458C>T intron_variant, non_coding_transcript_variant
DELEC1ENST00000649565.1 linkuse as main transcriptn.226-35528C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.495
AC:
75216
AN:
151962
Hom.:
19735
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.674
Gnomad AMI
AF:
0.468
Gnomad AMR
AF:
0.514
Gnomad ASJ
AF:
0.445
Gnomad EAS
AF:
0.257
Gnomad SAS
AF:
0.418
Gnomad FIN
AF:
0.414
Gnomad MID
AF:
0.392
Gnomad NFE
AF:
0.423
Gnomad OTH
AF:
0.460
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.495
AC:
75323
AN:
152084
Hom.:
19778
Cov.:
32
AF XY:
0.494
AC XY:
36761
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.674
Gnomad4 AMR
AF:
0.515
Gnomad4 ASJ
AF:
0.445
Gnomad4 EAS
AF:
0.256
Gnomad4 SAS
AF:
0.417
Gnomad4 FIN
AF:
0.414
Gnomad4 NFE
AF:
0.423
Gnomad4 OTH
AF:
0.463
Alfa
AF:
0.433
Hom.:
24543
Bravo
AF:
0.508
Asia WGS
AF:
0.424
AC:
1471
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
0.99
DANN
Benign
0.54

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: rs726657; hg19: chr9-117696336; API