rs10915216

Variant names:

• chr1-29030151-T-A
• rs10915216
• NM_001376013.1:c.1125-249T>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001376013.1(EPB41):​c.1125-249T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,636 control chromosomes in the GnomAD database, including 15,165 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.42 (15165 hom., cov: 30)
• Consequence: EPB41 NM_001376013.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.26
• Publications: 5 publications found

Genes affected

EPB41 (HGNC:3377): (erythrocyte membrane protein band 4.1) The protein encoded by this gene, together with spectrin and actin, constitute the red cell membrane cytoskeletal network. This complex plays a critical role in erythrocyte shape and deformability. Mutations in this gene are associated with type 1 elliptocytosis (EL1). Alternatively spliced transcript variants encoding different isoforms have been described for this gene.[provided by RefSeq, Oct 2009]

EPB41 Gene-Disease associations (from GenCC):

• elliptocytosis 1

  Inheritance: SD, AR, AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• hereditary elliptocytosis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 1-29030151-T-A is Benign according to our data. Variant chr1-29030151-T-A is described in ClinVar as Benign. ClinVar VariationId is 1282344.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPB41	NM_001376013.1	c.1125-249T>A		intron_variant	Intron 7 of 20	ENST00000343067.9	NP_001362942.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPB41	ENST00000343067.9	c.1125-249T>A		intron_variant	Intron 7 of 20	5	NM_001376013.1	ENSP00000345259.4

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63579 AN: 151518 Hom.: 15167 Cov.: 30

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.419 AC: 63593 AN: 151636 Hom.: 15165 Cov.: 30 AF XY: 0.432 AC XY: 32035 AN XY: 74074

African (AFR) AF: 0.190 AC: 7881 AN: 41404

American (AMR) AF: 0.484 AC: 7349 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1768 AN: 3468

East Asian (EAS) AF: 0.447 AC: 2300 AN: 5144

South Asian (SAS) AF: 0.560 AC: 2689 AN: 4806

European-Finnish (FIN) AF: 0.630 AC: 6587 AN: 10458

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33653 AN: 67874

Other (OTH) AF: 0.415 AC: 873 AN: 2104

Alfa AF: 0.458 Hom.: 2120

Bravo AF: 0.393

Asia WGS AF: 0.459 AC: 1595 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.034
DANN	Benign	0.37
PhyloP100		-2.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10915216; hg19: chr1-29356663;