NM_020775.5:c.1968C>T

Variant names:

• chr1-109194441-C-T
• rs2359246
• NM_020775.5:c.1968C>T

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 23 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020775.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELAPOR1	NM_020775.5	MANE Select	c.1968C>T	p.Asn656Asn	synonymous	Exon 15 of 22	NP_065826.3
	ELAPOR1	NM_001267048.2		c.1707C>T	p.Asn569Asn	synonymous	Exon 13 of 20	NP_001253977.2
	ELAPOR1	NM_001284352.2		c.1662C>T	p.Asn554Asn	synonymous	Exon 14 of 21	NP_001271281.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELAPOR1	ENST00000369939.8	TSL:5 MANE Select	c.1968C>T	p.Asn656Asn	synonymous	Exon 15 of 22	ENSP00000358955.3
	ELAPOR1	ENST00000529753.5	TSL:1	c.1707C>T	p.Asn569Asn	synonymous	Exon 13 of 20	ENSP00000434595.1
	ELAPOR1	ENST00000369936.2	TSL:1	n.1125C>T		non_coding_transcript_exon	Exon 7 of 14

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101776 AN: 152042 Hom.: 36875 Cov.: 33

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

GnomAD2 exomes AF: 0.784 AC: 197031 AN: 251342 AF XY: 0.789

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 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

African (AFR) AF: 0.352 AC: 11771 AN: 33426

American (AMR) AF: 0.843 AC: 37702 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 18549 AN: 26110

East Asian (EAS) AF: 0.979 AC: 38861 AN: 39698

South Asian (SAS) AF: 0.868 AC: 74876 AN: 86216

European-Finnish (FIN) AF: 0.839 AC: 44749 AN: 53362

Middle Eastern (MID) AF: 0.659 AC: 3794 AN: 5754

European-Non Finnish (NFE) AF: 0.766 AC: 849939 AN: 1109766

Other (OTH) AF: 0.749 AC: 45191 AN: 60312

GnomAD4 genome AF: 0.669 AC: 101824 AN: 152160 Hom.: 36892 Cov.: 33 AF XY: 0.678 AC XY: 50446 AN XY: 74404

African (AFR) AF: 0.370 AC: 15357 AN: 41478

American (AMR) AF: 0.753 AC: 11519 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2423 AN: 3468

East Asian (EAS) AF: 0.972 AC: 5021 AN: 5164

South Asian (SAS) AF: 0.877 AC: 4240 AN: 4834

European-Finnish (FIN) AF: 0.840 AC: 8904 AN: 10600

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52125 AN: 68006

Other (OTH) AF: 0.669 AC: 1413 AN: 2112

Alfa AF: 0.727 Hom.: 117269

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	0.24
DANN	Benign	0.68
PhyloP100		-2.2
Mutation Taster		=95/5	polymorphism (auto)

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

Other links and lift over

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