13-101493209-C-T

Variant names:

• chr13-101493209-C-T
• rs1335587
• NM_004791.3:c.316+39109C>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+39109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 151,938 control chromosomes in the GnomAD database, including 32,902 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 0.65 (32902 hom., cov: 31)
• Consequence: ITGBL1 NM_004791.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGBL1	NM_004791.3	c.316+39109C>T		intron_variant	Intron 2 of 10	ENST00000376180.8	NP_004782.1
ITGBL1	NM_001271755.2	c.316+39109C>T		intron_variant	Intron 2 of 9		NP_001258684.1
ITGBL1	NM_001271756.2	c.37+3209C>T		intron_variant	Intron 1 of 9		NP_001258685.1
ITGBL1	NM_001271754.2	c.-108+40278C>T		intron_variant	Intron 1 of 10		NP_001258683.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGBL1	ENST00000376180.8	c.316+39109C>T		intron_variant	Intron 2 of 10	1	NM_004791.3	ENSP00000365351.3
ITGBL1	ENST00000618057.4	c.316+39109C>T		intron_variant	Intron 2 of 9	1		ENSP00000481484.1
ITGBL1	ENST00000376162.7	c.37+3209C>T		intron_variant	Intron 1 of 9	2		ENSP00000365332.3
ITGBL1	ENST00000545560.6	c.-108+40278C>T		intron_variant	Intron 1 of 10	2		ENSP00000439903.1

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98869 AN: 151820 Hom.: 32843 Cov.: 31

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.652 AC: 98996 AN: 151938 Hom.: 32902 Cov.: 31 AF XY: 0.650 AC XY: 48298 AN XY: 74252

Gnomad4 AFR AF: 0.766

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.613

Alfa AF: 0.613 Hom.: 28925

Bravo AF: 0.648

Asia WGS AF: 0.463 AC: 1607 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.51

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: rs1335587; hg19: chr13-102145560;