chr13-101487185-C-T

Position:

• chr13-101487185-C-T

Variant summary

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

The NM_004791.3(ITGBL1):​c.316+33085C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 151,998 control chromosomes in the GnomAD database, including 4,904 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 0.24 (4904 hom., cov: 32)
• Consequence: ITGBL1 NM_004791.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221

Genes affected

ITGBL1 (HGNC:6164): (integrin subunit beta like 1) This gene encodes a beta integrin-related protein that is a member of the EGF-like protein family. The encoded protein contains integrin-like cysteine-rich repeats. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGBL1	NM_004791.3	c.316+33085C>T		intron_variant		ENST00000376180.8
ITGBL1	NM_001271754.2	c.-108+34254C>T		intron_variant
ITGBL1	NM_001271755.2	c.316+33085C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGBL1	ENST00000376180.8	c.316+33085C>T		intron_variant		1	NM_004791.3	P1
ITGBL1	ENST00000618057.4	c.316+33085C>T		intron_variant		1
ITGBL1	ENST00000545560.6	c.-108+34254C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36577 AN: 151880 Hom.: 4901 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.241 AC: 36604 AN: 151998 Hom.: 4904 Cov.: 32 AF XY: 0.244 AC XY: 18142 AN XY: 74278

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.257

Alfa AF: 0.204 Hom.: 1611

Bravo AF: 0.258

Asia WGS AF: 0.423 AC: 1467 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.49

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: rs10851132; hg19: chr13-102139536;