2-36740625-A-G

Variant names:

• chr2-36740625-A-G
• rs10490661
• NM_053276.4:c.119-2475A>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.119-2475A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0972 in 152,166 control chromosomes in the GnomAD database, including 1,477 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 0.097 (1477 hom., cov: 33)
• Consequence: VIT NM_053276.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VIT	NM_053276.4	c.119-2475A>G		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.119-2475A>G		intron_variant	Intron 3 of 15	2	NM_053276.4	ENSP00000368544.3

Frequencies

GnomAD3 genomes AF: 0.0971 AC: 14761 AN: 152048 Hom.: 1466 Cov.: 33

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.0479

Gnomad FIN AF: 0.0386

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0157

Gnomad OTH AF: 0.0801

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

GnomAD4 genome AF: 0.0972 AC: 14792 AN: 152166 Hom.: 1477 Cov.: 33 AF XY: 0.100 AC XY: 7469 AN XY: 74418

African (AFR) AF: 0.184 AC: 7628 AN: 41488

American (AMR) AF: 0.234 AC: 3566 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0170 AC: 59 AN: 3470

East Asian (EAS) AF: 0.305 AC: 1577 AN: 5174

South Asian (SAS) AF: 0.0473 AC: 228 AN: 4822

European-Finnish (FIN) AF: 0.0386 AC: 410 AN: 10614

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0157 AC: 1067 AN: 68016

Other (OTH) AF: 0.0793 AC: 167 AN: 2106

Alfa AF: 0.0452 Hom.: 2341

Bravo AF: 0.121

Asia WGS AF: 0.173 AC: 602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.36
PhyloP100		-0.13
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: rs10490661; hg19: chr2-36967768;