rs10915207

Variant names:

• chr1-28896865-C-G
• rs10915207
• ENST00000347529.7:c.-8+9655C>G

Your query was ambiguous. Multiple possible variants found:

• chr1-28896865-C-G
• chr1-28896865-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001166005.2(EPB41):​c.-8+9655C>G variant causes a intron 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: EPB41 NM_001166005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPB41	NM_001166005.2	c.-8+9655C>G		intron_variant	Intron 1 of 20		NP_001159477.1
EPB41	NM_203343.3	c.-8+9655C>G		intron_variant	Intron 1 of 16		NP_976218.1
EPB41	NM_001376022.1	c.-618+9655C>G		intron_variant	Intron 1 of 20		NP_001362951.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPB41	ENST00000347529.7	c.-8+9655C>G		intron_variant	Intron 1 of 16	1		ENSP00000290100.6
EPB41	ENST00000373800.7	c.-698+9655C>G		intron_variant	Intron 1 of 18	1		ENSP00000362906.3
EPB41	ENST00000373798.5	c.-8+3028C>G		intron_variant	Intron 1 of 20	5		ENSP00000362904.1

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.34
DANN	Benign	0.40

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: rs10915207; hg19: chr1-29223377;