NM_001114134.2:c.1852A>T

Variant names:

• chr15-43201905-T-A
• NM_001114134.2:c.1852A>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001114134.2(EPB42):​c.1852A>T​(p.Met618Leu) 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. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: EPB42 NM_001114134.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.467

Genes affected

EPB42 (HGNC:3381): (erythrocyte membrane protein band 4.2) Erythrocyte membrane protein band 4.2 is an ATP-binding protein which may regulate the association of protein 3 with ankyrin. It probably has a role in erythrocyte shape and mechanical property regulation. Mutations in the EPB42 gene are associated with recessive spherocytic elliptocytosis and recessively transmitted hereditary hemolytic anemia. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ENSG00000285117 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.10616645).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPB42	NM_001114134.2	c.1852A>T	p.Met618Leu	missense_variant	Exon 12 of 13	ENST00000441366.7	NP_001107606.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPB42	ENST00000441366.7	c.1852A>T	p.Met618Leu	missense_variant	Exon 12 of 13	1	NM_001114134.2	ENSP00000396616.2
ENSG00000285117	ENST00000563128.5	n.386A>T		non_coding_transcript_exon_variant	Exon 3 of 4	3		ENSP00000520455.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hereditary spherocytosis type 5 Uncertain:1

Mar 10, 2023

Revvity Omics, Revvity

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.084
BayesDel_addAF	Uncertain	0.14	D
BayesDel_noAF	Benign	-0.61
CADD	Benign	0.17
DANN	Benign	0.95
DEOGEN2	Benign	0.064	.;.;.;T;.
Eigen	Benign	-0.89
Eigen_PC	Benign	-0.75
FATHMM_MKL	Benign	0.38	N
LIST_S2	Benign	0.51	.;T;T;T;T
M_CAP	Benign	0.0042	T
MetaRNN	Benign	0.11	T;T;T;T;T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	0.89	.;.;.;L;.
PrimateAI	Benign	0.31	T
PROVEAN	Benign	0.13	.;.;N;N;.
REVEL	Benign	0.074
Sift	Benign	1.0	.;.;T;T;.
Sift4G	Benign	1.0	.;.;T;T;T
Polyphen		0.0010	B;B;B;B;.
Vest4		0.18, 0.17, 0.22
MutPred		0.68		.;.;.;Loss of disorder (P = 0.1913);.;
MVP		0.13
ClinPred		0.091	T
GERP RS		-0.91
Varity_R		0.079
gMVP		0.53

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr15-43494103;