2-36740625-A-G

Position:

• chr2-36740625-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.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

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=-0.88).
• 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/exons	MANE	Protein	UniProt
VIT	NM_053276.4	c.119-2475A>G		intron_variant		ENST00000379242.8	NP_444506.2
LOC124905990	XR_007086283.1	n.334+24007T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VIT	ENST00000379242.8	c.119-2475A>G		intron_variant		2	NM_053276.4	ENSP00000368544	A2

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

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.0170

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.0473

Gnomad4 FIN AF: 0.0386

Gnomad4 NFE AF: 0.0157

Gnomad4 OTH AF: 0.0793

Alfa AF: 0.0275 Hom.: 406

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

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: rs10490661; hg19: chr2-36967768;