chr7-158734955-C-T

Variant names:

• chr7-158734955-C-T
• rs2878802
• NM_001367773.1:c.2506-484G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367773.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ESYT2	NM_001367773.1	MANE Select	c.2506-484G>A		intron	N/A	NP_001354702.1
	ESYT2	NM_020728.3		c.2443-484G>A		intron	N/A	NP_065779.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ESYT2	ENST00000275418.13	TSL:5 MANE Select	c.2506-484G>A		intron	N/A	ENSP00000275418.8
	ESYT2	ENST00000251527.10	TSL:1	c.2443-484G>A		intron	N/A	ENSP00000251527.6
	ESYT2	ENST00000944355.1		c.2608-484G>A		intron	N/A	ENSP00000614414.1

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

African (AFR) AF: 0.705 AC: 29251 AN: 41498

American (AMR) AF: 0.882 AC: 13494 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2951 AN: 3470

East Asian (EAS) AF: 0.918 AC: 4760 AN: 5186

South Asian (SAS) AF: 0.862 AC: 4161 AN: 4828

European-Finnish (FIN) AF: 0.869 AC: 9210 AN: 10600

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.866 AC: 58935 AN: 68032

Other (OTH) AF: 0.846 AC: 1786 AN: 2112

Alfa AF: 0.852 Hom.: 126010

Bravo AF: 0.819

Asia WGS AF: 0.887 AC: 3084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.010
DANN	Benign	0.55
PhyloP100		-1.3
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: rs2878802; hg19: chr7-158527646;