chr1-109194441-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_020775.5(ELAPOR1):​c.1968C>T​(p.Asn656Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 1,611,524 control chromosomes in the GnomAD database, including 476,407 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 0.67 ( 36892 hom., cov: 33)
Exomes 𝑓: 0.77 ( 439515 hom. )

Consequence

ELAPOR1
NM_020775.5 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.19
Variant links:
Genes affected
ELAPOR1 (HGNC:29618): (endosome-lysosome associated apoptosis and autophagy regulator 1) Expression of this gene is induced by estrogen and the encoded protein has been characterized as a transmembrane protein. The encoded protein has been found in to correlate with survival in certain carcinomas (PMID: 21102415) and may be important for cellular response to stress (PMID: 21072319). Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2012]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP7
Synonymous conserved (PhyloP=-2.18 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ELAPOR1NM_020775.5 linkc.1968C>T p.Asn656Asn synonymous_variant Exon 15 of 22 ENST00000369939.8 NP_065826.3 Q6UXG2-1B4DWM4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ELAPOR1ENST00000369939.8 linkc.1968C>T p.Asn656Asn synonymous_variant Exon 15 of 22 5 NM_020775.5 ENSP00000358955.3 Q6UXG2-1

Frequencies

GnomAD3 genomes
AF:
0.669
AC:
101776
AN:
152042
Hom.:
36875
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.371
Gnomad AMI
AF:
0.701
Gnomad AMR
AF:
0.753
Gnomad ASJ
AF:
0.699
Gnomad EAS
AF:
0.972
Gnomad SAS
AF:
0.877
Gnomad FIN
AF:
0.840
Gnomad MID
AF:
0.608
Gnomad NFE
AF:
0.766
Gnomad OTH
AF:
0.667
GnomAD3 exomes
AF:
0.784
AC:
197031
AN:
251342
Hom.:
79374
AF XY:
0.789
AC XY:
107206
AN XY:
135842
show subpopulations
Gnomad AFR exome
AF:
0.364
Gnomad AMR exome
AF:
0.853
Gnomad ASJ exome
AF:
0.705
Gnomad EAS exome
AF:
0.971
Gnomad SAS exome
AF:
0.872
Gnomad FIN exome
AF:
0.840
Gnomad NFE exome
AF:
0.766
Gnomad OTH exome
AF:
0.773
GnomAD4 exome
AF:
0.771
AC:
1125432
AN:
1459364
Hom.:
439515
Cov.:
51
AF XY:
0.774
AC XY:
562389
AN XY:
726144
show subpopulations
Gnomad4 AFR exome
AF:
0.352
Gnomad4 AMR exome
AF:
0.843
Gnomad4 ASJ exome
AF:
0.710
Gnomad4 EAS exome
AF:
0.979
Gnomad4 SAS exome
AF:
0.868
Gnomad4 FIN exome
AF:
0.839
Gnomad4 NFE exome
AF:
0.766
Gnomad4 OTH exome
AF:
0.749
GnomAD4 genome
AF:
0.669
AC:
101824
AN:
152160
Hom.:
36892
Cov.:
33
AF XY:
0.678
AC XY:
50446
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.370
Gnomad4 AMR
AF:
0.753
Gnomad4 ASJ
AF:
0.699
Gnomad4 EAS
AF:
0.972
Gnomad4 SAS
AF:
0.877
Gnomad4 FIN
AF:
0.840
Gnomad4 NFE
AF:
0.766
Gnomad4 OTH
AF:
0.669
Alfa
AF:
0.733
Hom.:
54567
Bravo
AF:
0.650
Asia WGS
AF:
0.880
AC:
3059
AN:
3478
EpiCase
AF:
0.754
EpiControl
AF:
0.747

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.41
CADD
Benign
0.24
DANN
Benign
0.68

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.070
Details are displayed if max score is > 0.2

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: rs2359246; hg19: chr1-109737063; COSMIC: COSV64040793; COSMIC: COSV64040793; API