3-55537732-G-A

Variant names:

• chr3-55537732-G-A
• rs1795648
• NM_015576.3:c.*40-26456C>T

Variant summary

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

The NM_015576.3(ERC2):​c.*40-26456C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 152,094 control chromosomes in the GnomAD database, including 33,675 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 0.65 (33675 hom., cov: 33)
• Consequence: ERC2 NM_015576.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.685
• Publications: 15 publications found

Genes affected

ERC2 (HGNC:31922): (ELKS/RAB6-interacting/CAST family member 2) This gene encodes a protein that belongs to the Rab3-interacting molecule (RIM)-binding protein family. Members of this protein family form part of the cytomatrix at the active zone (CAZ) complex and function as regulators of neurotransmitter release. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015576.3. 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
	ERC2	NM_015576.3	MANE Select	c.*40-26456C>T		intron	N/A	NP_056391.1
	ERC2	NR_132749.2		n.3461-26456C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERC2	ENST00000288221.11	TSL:1 MANE Select	c.*40-26456C>T		intron	N/A	ENSP00000288221.6
	ERC2	ENST00000460849.5	TSL:1	n.*227-26456C>T		intron	N/A	ENSP00000417445.1
	ERC2	ENST00000484530.5	TSL:1	n.552-26456C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98909 AN: 151976 Hom.: 33659 Cov.: 33

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.651 AC: 98975 AN: 152094 Hom.: 33675 Cov.: 33 AF XY: 0.657 AC XY: 48865 AN XY: 74354

African (AFR) AF: 0.434 AC: 17987 AN: 41450

American (AMR) AF: 0.680 AC: 10396 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2727 AN: 3468

East Asian (EAS) AF: 0.833 AC: 4306 AN: 5168

South Asian (SAS) AF: 0.715 AC: 3444 AN: 4814

European-Finnish (FIN) AF: 0.787 AC: 8339 AN: 10592

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49532 AN: 67994

Other (OTH) AF: 0.680 AC: 1438 AN: 2114

Alfa AF: 0.711 Hom.: 116844

Bravo AF: 0.632

Asia WGS AF: 0.754 AC: 2619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.1
DANN	Benign	0.82
PhyloP100		0.69
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: rs1795648; hg19: chr3-55571760;