rs2359245

chr1-109194468-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_020775.5(ELAPOR1):c.1995G>A(p.Pro665=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 1,611,922 control chromosomes in the GnomAD database, including 476,261 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 (36875 hom., cov: 33)
  • Exomes 𝑓: 0.77 (439386 hom.)
• Consequence: ELAPOR1 NM_020775.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

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]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BP7: Synonymous conserved (PhyloP=-1.29 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/exons	MANE	UniProt
ELAPOR1	NM_020775.5	c.1995G>A	p.Pro665=	synonymous_variant	15/22	ENST00000369939.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELAPOR1	ENST00000369939.8	c.1995G>A	p.Pro665=	synonymous_variant	15/22	5	NM_020775.5	P1

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101773 AN: 151986 Hom.: 36857 Cov.: 33

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.665

GnomAD3 exomes AF: 0.784 AC: 197052 AN: 251430 Hom.: 79368 AF XY: 0.789 AC XY: 107204 AN XY: 135882

Gnomad AFR exome AF: 0.364

Gnomad AMR exome AF: 0.852

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: 1125475 AN: 1459818 Hom.: 439386 Cov.: 52 AF XY: 0.774 AC XY: 562418 AN XY: 726378

Gnomad4 AFR exome AF: 0.349

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: 101822 AN: 152104 Hom.: 36875 Cov.: 33 AF XY: 0.679 AC XY: 50454 AN XY: 74356

Gnomad4 AFR AF: 0.371

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: 0.668

Alfa AF: 0.729 Hom.: 38219

Bravo AF: 0.650

Asia WGS AF: 0.880 AC: 3059 AN: 3478

EpiCase AF: 0.753

EpiControl AF: 0.747

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	0.038
Dann	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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

Other links and lift over

dbSNP: rs2359245; hg19: chr1-109737090;