rs11878602

chr19-16444342-A-C

Variant summary

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

The NM_001258374.3(EPS15L1):c.34-2123T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,928 control chromosomes in the GnomAD database, including 15,783 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 0.42 (15783 hom., cov: 31)
• Consequence: EPS15L1 NM_001258374.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

Genes affected

EPS15L1 (HGNC:24634): (epidermal growth factor receptor pathway substrate 15 like 1) Enables cadherin binding activity. Predicted to be involved in endocytosis and endosomal transport. Located in 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPS15L1	NM_001258374.3	c.34-2123T>G		intron_variant		ENST00000455140.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPS15L1	ENST00000455140.7	c.34-2123T>G		intron_variant		2	NM_001258374.3	P1

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63762 AN: 151810 Hom.: 15732 Cov.: 31

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.420 AC: 63877 AN: 151928 Hom.: 15783 Cov.: 31 AF XY: 0.419 AC XY: 31144 AN XY: 74268

Gnomad4 AFR AF: 0.694

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.367

Alfa AF: 0.322 Hom.: 3995

Bravo AF: 0.437

Asia WGS AF: 0.369 AC: 1283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.33
Dann	Benign	0.38

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: rs11878602; hg19: chr19-16555153;