chr2-36752369-A-G

Position:

• chr2-36752369-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VIT	NM_053276.4	c.276-2552A>G		intron_variant		ENST00000379242.8	NP_444506.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VIT	ENST00000379242.8	c.276-2552A>G		intron_variant		2	NM_053276.4	ENSP00000368544.3

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

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.924

Gnomad4 ASJ AF: 0.915

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.877

Gnomad4 OTH AF: 0.874

Alfa AF: 0.881 Hom.: 79476

Bravo AF: 0.869

Asia WGS AF: 0.862 AC: 2997 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	3.9
DANN	Benign	0.37

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: rs4670600; hg19: chr2-36979512;