rs10460526

Variant names:

• chr2-36705700-C-T
• rs10460526
• NM_053276.4:c.-19+8727C>T

Variant summary

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

The NM_053276.4(VIT):​c.-19+8727C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,096 control chromosomes in the GnomAD database, including 8,316 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 (8316 hom., cov: 32)
• Consequence: VIT NM_053276.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_053276.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VIT	NM_053276.4	MANE Select	c.-19+8727C>T		intron	N/A	NP_444506.2
	VIT	NM_001177969.2		c.-19+8727C>T		intron	N/A	NP_001171440.1
	VIT	NM_001328661.2		c.-19+8727C>T		intron	N/A	NP_001315590.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VIT	ENST00000379242.8	TSL:2 MANE Select	c.-19+8727C>T		intron	N/A	ENSP00000368544.3
	VIT	ENST00000389975.7	TSL:1	c.-19+8727C>T		intron	N/A	ENSP00000374625.3
	VIT	ENST00000401530.5	TSL:1	c.-19+8727C>T		intron	N/A	ENSP00000385658.1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47234 AN: 151978 Hom.: 8320 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.310 AC: 47219 AN: 152096 Hom.: 8316 Cov.: 32 AF XY: 0.311 AC XY: 23136 AN XY: 74316

African (AFR) AF: 0.142 AC: 5887 AN: 41524

American (AMR) AF: 0.320 AC: 4884 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1578 AN: 3466

East Asian (EAS) AF: 0.239 AC: 1237 AN: 5170

South Asian (SAS) AF: 0.433 AC: 2084 AN: 4814

European-Finnish (FIN) AF: 0.359 AC: 3791 AN: 10556

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.392 AC: 26613 AN: 67966

Other (OTH) AF: 0.332 AC: 703 AN: 2116

Alfa AF: 0.382 Hom.: 18524

Bravo AF: 0.296

Asia WGS AF: 0.327 AC: 1138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.46
PhyloP100		-2.0
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: rs10460526; hg19: chr2-36932843;