rs2878802

chr7-158734955-C-T

Variant summary

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

The NM_001367773.1(ESYT2):c.2506-484G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,232 control chromosomes in the GnomAD database, including 52,181 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 0.82 (52181 hom., cov: 33)
• Consequence: ESYT2 NM_001367773.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

ESYT2 (HGNC:22211): (extended synaptotagmin 2) Enables calcium ion binding activity; identical protein binding activity; and phospholipid binding activity. Predicted to be involved in endocytosis; endoplasmic reticulum-plasma membrane tethering; and lipid transport. Located in endoplasmic reticulum-plasma membrane contact site. Is extrinsic component of cytoplasmic side of plasma membrane; integral component of plasma membrane; and intrinsic component of endoplasmic reticulum 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ESYT2	NM_001367773.1	c.2506-484G>A		intron_variant		ENST00000275418.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ESYT2	ENST00000275418.13	c.2506-484G>A		intron_variant		5	NM_001367773.1
ESYT2	ENST00000251527.10	c.2443-484G>A		intron_variant		1		P2
ESYT2	ENST00000652148.1	c.2587-484G>A		intron_variant				A2
ESYT2	ENST00000435514.3	n.1401-484G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125408 AN: 152114 Hom.: 52160 Cov.: 33

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.824 AC: 125467 AN: 152232 Hom.: 52181 Cov.: 33 AF XY: 0.825 AC XY: 61360 AN XY: 74420

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.850

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.862

Gnomad4 FIN AF: 0.869

Gnomad4 NFE AF: 0.866

Gnomad4 OTH AF: 0.846

Alfa AF: 0.854 Hom.: 44888

Bravo AF: 0.819

Asia WGS AF: 0.887 AC: 3084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.010
Dann	Benign	0.55

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: rs2878802; hg19: chr7-158527646;