rs11691187

chr2-36713453-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_053276.4(VIT):c.-18-2900C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,100 control chromosomes in the GnomAD database, including 8,575 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 0.31 (8575 hom., cov: 32)
• Consequence: VIT NM_053276.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156

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 (NFE) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VIT	NM_053276.4	c.-18-2900C>T		intron_variant		ENST00000379242.8
LOC124905990	XR_007086283.1	n.335-23793G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VIT	ENST00000379242.8	c.-18-2900C>T		intron_variant		2	NM_053276.4	A2

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46717 AN: 151982 Hom.: 8584 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.307 AC: 46707 AN: 152100 Hom.: 8575 Cov.: 32 AF XY: 0.308 AC XY: 22933 AN XY: 74342

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.339

Alfa AF: 0.384 Hom.: 15518

Bravo AF: 0.285

Asia WGS AF: 0.307 AC: 1066 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	3.5
Dann	Benign	0.68

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: rs11691187; hg19: chr2-36940596;