9-109230229-C-T

Variant summary

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

The NM_019114.5(EPB41L4B):c.1410-13084G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,200 control chromosomes in the GnomAD database, including 1,720 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 0.13 (1720 hom., cov: 32)
• Consequence: EPB41L4B NM_019114.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386

Genes affected

EPB41L4B (HGNC:19818): (erythrocyte membrane protein band 4.1 like 4B) Predicted to be a structural constituent of cytoskeleton. Involved in several processes, including positive regulation of cell adhesion; positive regulation of keratinocyte migration; and wound healing. Acts upstream of or within actomyosin structure organization. Located in apical part of cell; cytosol; 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPB41L4B	NM_019114.5	c.1410-13084G>A		intron_variant		ENST00000374566.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPB41L4B	ENST00000374566.8	c.1410-13084G>A		intron_variant		1	NM_019114.5	P3

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19937 AN: 152082 Hom.: 1720 Cov.: 32

Gnomad AFR AF: 0.0310

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.131 AC: 19941 AN: 152200 Hom.: 1720 Cov.: 32 AF XY: 0.132 AC XY: 9830 AN XY: 74412

Gnomad4 AFR AF: 0.0308

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0850

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.141

Alfa AF: 0.153 Hom.: 2782

Bravo AF: 0.123

Asia WGS AF: 0.193 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	5.5
Dann	Benign	0.26

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: rs10816789; hg19: chr9-111992509;