chr1-109161931-C-G

Variant names:

• chr1-109161931-C-G
• rs752023385
• NM_020775.5:c.191C>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_020775.5(ELAPOR1):​c.191C>G​(p.Thr64Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T64M) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 34)
• Consequence: ELAPOR1 NM_020775.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.454
• Publications: 1 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.09789616).

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.191C>G	p.Thr64Arg	missense	Exon 2 of 22	NP_065826.3
	ELAPOR1	NM_001267048.2		c.191C>G	p.Thr64Arg	missense	Exon 2 of 20	NP_001253977.2	Q6UXG2-3
	ELAPOR1	NM_001284352.2		c.-32-2568C>G		intron	N/A	NP_001271281.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELAPOR1	ENST00000369939.8	TSL:5 MANE Select	c.191C>G	p.Thr64Arg	missense	Exon 2 of 22	ENSP00000358955.3	Q6UXG2-1
	ELAPOR1	ENST00000529753.5	TSL:1	c.191C>G	p.Thr64Arg	missense	Exon 2 of 20	ENSP00000434595.1	Q6UXG2-3
	ELAPOR1	ENST00000899218.1		c.191C>G	p.Thr64Arg	missense	Exon 3 of 23	ENSP00000569277.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.078
BayesDel_addAF	Benign	-0.15	T
BayesDel_noAF	Benign	-0.45
CADD	Benign	16
DANN	Benign	0.97
DEOGEN2	Benign	0.062	T
Eigen	Benign	-0.53
Eigen_PC	Benign	-0.50
FATHMM_MKL	Benign	0.12	N
LIST_S2	Benign	0.74	T
M_CAP	Benign	0.010	T
MetaRNN	Benign	0.098	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.3	L
PhyloP100		0.45
PrimateAI	Uncertain	0.50	T
PROVEAN	Uncertain	-3.2	D
REVEL	Benign	0.085
Sift	Uncertain	0.023	D
Sift4G	Benign	0.074	T
Polyphen		0.45	B
Vest4		0.30
MutPred		0.33		Gain of phosphorylation at S66 (P = 0.0658)
MVP		0.24
MPC		0.32
ClinPred		0.50	D
GERP RS		1.1
Varity_R		0.11
gMVP		0.33
Mutation Taster		=92/8	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.14		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: rs752023385; hg19: chr1-109704553;