rs1464766

Variant names:

• chr5-112277645-A-G
• rs1464766
• NM_022140.5:c.257-2241T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-112277645-A-G
• chr5-112277645-A-T

Variant summary

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

The NM_022140.5(EPB41L4A):​c.257-2241T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 152,068 control chromosomes in the GnomAD database, including 27,644 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 0.59 (27644 hom., cov: 31)
• Consequence: EPB41L4A NM_022140.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272
• Publications: 3 publications found

Genes affected

EPB41L4A (HGNC:13278): (erythrocyte membrane protein band 4.1 like 4A) The protein encoded by this gene is a member of the band 4.1 protein superfamily. Members of this superfamily are thought to play an important role in regulating interactions between the cytoskeleton and plasma membrane, and contain an amino terminal conserved domain that binds glycophorin C. This gene product is thought to be involved in the beta-catenin signaling pathway. [provided by RefSeq, Dec 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPB41L4A	NM_022140.5	c.257-2241T>C		intron_variant	Intron 3 of 22	ENST00000261486.6	NP_071423.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPB41L4A	ENST00000261486.6	c.257-2241T>C		intron_variant	Intron 3 of 22	1	NM_022140.5	ENSP00000261486.5
EPB41L4A	ENST00000305368.8	n.531-2241T>C		intron_variant	Intron 3 of 5	1
EPB41L4A	ENST00000512395.5	n.220-2241T>C		intron_variant	Intron 3 of 6	4
EPB41L4A	ENST00000514203.1	n.70-2241T>C		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90092 AN: 151950 Hom.: 27633 Cov.: 31

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.593 AC: 90145 AN: 152068 Hom.: 27644 Cov.: 31 AF XY: 0.600 AC XY: 44605 AN XY: 74330

African (AFR) AF: 0.429 AC: 17783 AN: 41484

American (AMR) AF: 0.643 AC: 9819 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2520 AN: 3470

East Asian (EAS) AF: 0.645 AC: 3339 AN: 5178

South Asian (SAS) AF: 0.754 AC: 3629 AN: 4810

European-Finnish (FIN) AF: 0.715 AC: 7562 AN: 10580

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43503 AN: 67968

Other (OTH) AF: 0.622 AC: 1307 AN: 2102

Alfa AF: 0.612 Hom.: 50057

Bravo AF: 0.575

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.64
PhyloP100		-0.27
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: rs1464766; hg19: chr5-111613342;