chr7-158735911-A-G

Variant names:

• chr7-158735911-A-G
• rs3816465
• NM_001367773.1:c.2400-303T>C

Variant summary

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

The NM_001367773.1(ESYT2):​c.2400-303T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 151,984 control chromosomes in the GnomAD database, including 39,300 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 0.71 (39300 hom., cov: 31)
• Consequence: ESYT2 NM_001367773.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 5 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 (NFE) allele frequency at 95% confidence interval = 0.784 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ESYT2	NM_001367773.1	MANE Select	c.2400-303T>C		intron	N/A	NP_001354702.1
	ESYT2	NM_020728.3		c.2337-303T>C		intron	N/A	NP_065779.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ESYT2	ENST00000275418.13	TSL:5 MANE Select	c.2400-303T>C		intron	N/A	ENSP00000275418.8
	ESYT2	ENST00000251527.10	TSL:1	c.2337-303T>C		intron	N/A	ENSP00000251527.6
	ESYT2	ENST00000652148.1		c.2481-303T>C		intron	N/A	ENSP00000499020.1

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107813 AN: 151866 Hom.: 39293 Cov.: 31

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.710 AC: 107874 AN: 151984 Hom.: 39300 Cov.: 31 AF XY: 0.707 AC XY: 52465 AN XY: 74252

African (AFR) AF: 0.586 AC: 24297 AN: 41428

American (AMR) AF: 0.747 AC: 11398 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2627 AN: 3472

East Asian (EAS) AF: 0.361 AC: 1864 AN: 5166

South Asian (SAS) AF: 0.660 AC: 3173 AN: 4810

European-Finnish (FIN) AF: 0.782 AC: 8246 AN: 10546

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.789 AC: 53665 AN: 67976

Other (OTH) AF: 0.725 AC: 1533 AN: 2114

Alfa AF: 0.754 Hom.: 22418

Bravo AF: 0.700

Asia WGS AF: 0.510 AC: 1777 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	0.55
DANN	Benign	0.49
PhyloP100		-1.0
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: rs3816465; hg19: chr7-158528602;