rs4897472

Variant names:

• chr6-130891998-G-A
• rs4897472
• NM_001431.4:c.1488-1532C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-130891998-G-A
• chr6-130891998-G-C
• chr6-130891998-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001431.4(EPB41L2):​c.1488-1532C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,026 control chromosomes in the GnomAD database, including 16,256 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 0.44 (16256 hom., cov: 32)
• Consequence: EPB41L2 NM_001431.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 6 publications found

Genes affected

EPB41L2 (HGNC:3379): (erythrocyte membrane protein band 4.1 like 2) Predicted to enable PH domain binding activity; cytoskeletal protein binding activity; and structural molecule activity. Involved in positive regulation of protein localization to cell cortex. Located in cell junction; nucleoplasm; and plasma membrane. Colocalizes with COP9 signalosome. [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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001431.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPB41L2	NM_001431.4	MANE Select	c.1488-1532C>T		intron	N/A	NP_001422.1
	EPB41L2	NM_001350299.2		c.1488-1532C>T		intron	N/A	NP_001337228.1
	EPB41L2	NM_001350301.2		c.1488-1532C>T		intron	N/A	NP_001337230.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPB41L2	ENST00000337057.8	TSL:1 MANE Select	c.1488-1532C>T		intron	N/A	ENSP00000338481.3
	EPB41L2	ENST00000528282.5	TSL:1	c.1488-1532C>T		intron	N/A	ENSP00000434308.1
	EPB41L2	ENST00000392427.7	TSL:1	c.1488-1532C>T		intron	N/A	ENSP00000376222.3

Frequencies

GnomAD3 genomes AF: 0.441 AC: 67010 AN: 151908 Hom.: 16237 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.441 AC: 67062 AN: 152026 Hom.: 16256 Cov.: 32 AF XY: 0.448 AC XY: 33327 AN XY: 74308

African (AFR) AF: 0.236 AC: 9800 AN: 41454

American (AMR) AF: 0.460 AC: 7023 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1582 AN: 3470

East Asian (EAS) AF: 0.510 AC: 2627 AN: 5156

South Asian (SAS) AF: 0.515 AC: 2477 AN: 4812

European-Finnish (FIN) AF: 0.655 AC: 6906 AN: 10546

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35216 AN: 67990

Other (OTH) AF: 0.425 AC: 898 AN: 2112

Alfa AF: 0.354 Hom.: 3785

Bravo AF: 0.416

Asia WGS AF: 0.504 AC: 1751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.34
PhyloP100		0.12
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: rs4897472; hg19: chr6-131213138; COSMIC: COSV61358538; COSMIC: COSV61358538;