NM_053276.4:c.119-3894T>C

Variant names:

• chr2-36739206-T-C
• rs10490662
• NM_053276.4:c.119-3894T>C

Variant summary

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

The NM_053276.4(VIT):​c.119-3894T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0987 in 152,174 control chromosomes in the GnomAD database, including 1,578 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 0.099 (1578 hom., cov: 32)
• Consequence: VIT NM_053276.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301
• Publications: 1 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VIT	NM_053276.4	c.119-3894T>C		intron_variant	Intron 3 of 15	ENST00000379242.8	NP_444506.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VIT	ENST00000379242.8	c.119-3894T>C		intron_variant	Intron 3 of 15	2	NM_053276.4	ENSP00000368544.3

Frequencies

GnomAD3 genomes AF: 0.0986 AC: 14990 AN: 152056 Hom.: 1569 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.0421

Gnomad FIN AF: 0.0223

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0123

Gnomad OTH AF: 0.0862

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

GnomAD4 genome AF: 0.0987 AC: 15025 AN: 152174 Hom.: 1578 Cov.: 32 AF XY: 0.101 AC XY: 7501 AN XY: 74392

African (AFR) AF: 0.204 AC: 8461 AN: 41472

American (AMR) AF: 0.237 AC: 3625 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0349 AC: 121 AN: 3470

East Asian (EAS) AF: 0.259 AC: 1339 AN: 5170

South Asian (SAS) AF: 0.0413 AC: 199 AN: 4822

European-Finnish (FIN) AF: 0.0223 AC: 237 AN: 10612

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0123 AC: 834 AN: 68030

Other (OTH) AF: 0.0853 AC: 180 AN: 2110

Alfa AF: 0.0592 Hom.: 521

Bravo AF: 0.125

Asia WGS AF: 0.145 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	14
DANN	Benign	0.77
PhyloP100		0.30
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: rs10490662; hg19: chr2-36966349;