2-120153444-G-T

Variant names:

• chr2-120153444-G-T
• rs7584209
• NM_020909.4:c.1793+7155G>T

Variant summary

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

The NM_020909.4(EPB41L5):​c.1793+7155G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 151,896 control chromosomes in the GnomAD database, including 32,095 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 0.64 (32095 hom., cov: 31)
• Consequence: EPB41L5 NM_020909.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

Genes affected

EPB41L5 (HGNC:19819): (erythrocyte membrane protein band 4.1 like 5) Predicted to enable cytoskeletal protein binding activity and protein domain specific binding activity. Predicted to be involved in actomyosin structure organization. Predicted to act upstream of or within several processes, including chordate embryonic development; embryonic foregut morphogenesis; and mesoderm morphogenesis. Located in cytosol; nucleoplasm; and plasma 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 (NFE) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPB41L5	NM_020909.4	c.1793+7155G>T		intron_variant	Intron 20 of 24	ENST00000263713.10	NP_065960.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPB41L5	ENST00000263713.10	c.1793+7155G>T		intron_variant	Intron 20 of 24	1	NM_020909.4	ENSP00000263713.5
EPB41L5	ENST00000452780.1	c.1793+7155G>T		intron_variant	Intron 19 of 23	5		ENSP00000390439.1
EPB41L5	ENST00000443902.6	c.1793+7155G>T		intron_variant	Intron 20 of 23	2		ENSP00000393856.2

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96644 AN: 151780 Hom.: 32097 Cov.: 31

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.745

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.636 AC: 96669 AN: 151896 Hom.: 32095 Cov.: 31 AF XY: 0.635 AC XY: 47171 AN XY: 74244

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.689

Alfa AF: 0.660 Hom.: 4198

Bravo AF: 0.632

Asia WGS AF: 0.644 AC: 2231 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.41
DANN	Benign	0.41

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: rs7584209; hg19: chr2-120911020;