2-120153444-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020909.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPB41L5	NM_020909.4	MANE Select	c.1793+7155G>T		intron	N/A	NP_065960.2
	EPB41L5	NM_001330310.2		c.1793+7155G>T		intron	N/A	NP_001317239.1	Q9HCM4-3
	EPB41L5	NM_001184937.2		c.1793+7155G>T		intron	N/A	NP_001171866.1	Q9HCM4-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPB41L5	ENST00000263713.10	TSL:1 MANE Select	c.1793+7155G>T		intron	N/A	ENSP00000263713.5	Q9HCM4-1
	EPB41L5	ENST00000851970.1		c.1793+7155G>T		intron	N/A	ENSP00000522029.1
	EPB41L5	ENST00000851976.1		c.1793+7155G>T		intron	N/A	ENSP00000522035.1

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

African (AFR) AF: 0.440 AC: 18234 AN: 41414

American (AMR) AF: 0.684 AC: 10442 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2902 AN: 3470

East Asian (EAS) AF: 0.708 AC: 3662 AN: 5174

South Asian (SAS) AF: 0.616 AC: 2967 AN: 4818

European-Finnish (FIN) AF: 0.676 AC: 7117 AN: 10522

Middle Eastern (MID) AF: 0.743 AC: 217 AN: 292

European-Non Finnish (NFE) AF: 0.721 AC: 48951 AN: 67912

Other (OTH) AF: 0.689 AC: 1452 AN: 2108

Alfa AF: 0.650 Hom.: 4269

Bravo AF: 0.632

Asia WGS AF: 0.644 AC: 2231 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.41
DANN	Benign	0.41
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: rs7584209; hg19: chr2-120911020;