2-36752369-A-G

Variant names:

• chr2-36752369-A-G
• rs4670600
• NM_053276.4:c.276-2552A>G

Variant summary

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

The NM_053276.4(VIT):​c.276-2552A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.869 in 152,104 control chromosomes in the GnomAD database, including 57,456 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 0.87 (57456 hom., cov: 30)
• Consequence: VIT NM_053276.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 2 publications found

Genes affected

VIT (HGNC:12697): (vitrin) This gene encodes an extracellular matrix (ECM) protein. The protein may be associated with cell adhesion and migration. High levels of expression of the protein in specific parts of the brain suggest its likely role in neural development. [provided by RefSeq, Jun 2016]

LOC124905990 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_053276.4. 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
	VIT	NM_053276.4	MANE Select	c.276-2552A>G		intron	N/A	NP_444506.2
	VIT	NM_001177969.2		c.276-2552A>G		intron	N/A	NP_001171440.1
	VIT	NM_001328661.2		c.276-2552A>G		intron	N/A	NP_001315590.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VIT	ENST00000379242.8	TSL:2 MANE Select	c.276-2552A>G		intron	N/A	ENSP00000368544.3
	VIT	ENST00000389975.7	TSL:1	c.276-2552A>G		intron	N/A	ENSP00000374625.3
	VIT	ENST00000401530.5	TSL:1	c.276-2552A>G		intron	N/A	ENSP00000385658.1

Frequencies

GnomAD3 genomes AF: 0.869 AC: 132013 AN: 151986 Hom.: 57417 Cov.: 30

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.869 AC: 132105 AN: 152104 Hom.: 57456 Cov.: 30 AF XY: 0.871 AC XY: 64746 AN XY: 74358

African (AFR) AF: 0.834 AC: 34592 AN: 41484

American (AMR) AF: 0.924 AC: 14123 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 3176 AN: 3472

East Asian (EAS) AF: 0.856 AC: 4425 AN: 5170

South Asian (SAS) AF: 0.864 AC: 4160 AN: 4814

European-Finnish (FIN) AF: 0.868 AC: 9182 AN: 10584

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.877 AC: 59591 AN: 67982

Other (OTH) AF: 0.874 AC: 1844 AN: 2110

Alfa AF: 0.878 Hom.: 114686

Bravo AF: 0.869

Asia WGS AF: 0.862 AC: 2997 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	3.9
DANN	Benign	0.37
PhyloP100		-0.055
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: rs4670600; hg19: chr2-36979512;