rs1476455

Positions:

• chr7-86922424-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142749.3(ELAPOR2):​c.1399+3104G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 151,304 control chromosomes in the GnomAD database, including 5,613 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 0.21 (5613 hom., cov: 32)
• Consequence: ELAPOR2 NM_001142749.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

Genes affected

ELAPOR2 (HGNC:21945): (endosome-lysosome associated apoptosis and autophagy regulator family member 2) Predicted to enable BMP receptor binding activity. Predicted to be involved in negative regulation of nervous system development; positive regulation of BMP signaling pathway; and positive regulation of epidermis development. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELAPOR2	NM_001142749.3	c.1399+3104G>T		intron_variant		ENST00000450689.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELAPOR2	ENST00000450689.7	c.1399+3104G>T		intron_variant		5	NM_001142749.3	P2

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32324 AN: 151190 Hom.: 5591 Cov.: 32

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.174

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.214 AC: 32396 AN: 151304 Hom.: 5613 Cov.: 32 AF XY: 0.210 AC XY: 15532 AN XY: 73916

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.173

Alfa AF: 0.174 Hom.: 471

Bravo AF: 0.228

Asia WGS AF: 0.132 AC: 451 AN: 3408

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.20

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs1476455; hg19: chr7-86551740;