rs10508070

Positions:

• chr13-101634281-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_004791.3(ITGBL1):​c.1015+35982G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00539 in 152,256 control chromosomes in the GnomAD database, including 4 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 0.0054 (4 hom., cov: 32)
• Consequence: ITGBL1 NM_004791.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BS2: High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGBL1	NM_004791.3	c.1015+35982G>A		intron_variant		ENST00000376180.8	NP_004782.1
ITGBL1	NM_001271754.2	c.592+35982G>A		intron_variant			NP_001258683.1
ITGBL1	NM_001271755.2	c.868+35982G>A		intron_variant			NP_001258684.1
ITGBL1	NM_001271756.2	c.736+35982G>A		intron_variant			NP_001258685.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGBL1	ENST00000376180.8	c.1015+35982G>A		intron_variant		1	NM_004791.3	ENSP00000365351	P1

Frequencies

GnomAD3 genomes AF: 0.00540 AC: 821 AN: 152138 Hom.: 4 Cov.: 32

Gnomad AFR AF: 0.00169

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00360

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00226

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00826

Gnomad OTH AF: 0.00574

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

GnomAD4 genome AF: 0.00539 AC: 820 AN: 152256 Hom.: 4 Cov.: 32 AF XY: 0.00477 AC XY: 355 AN XY: 74454

Gnomad4 AFR AF: 0.00168

Gnomad4 AMR AF: 0.00360

Gnomad4 ASJ AF: 0.0277

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000415

Gnomad4 FIN AF: 0.00226

Gnomad4 NFE AF: 0.00825

Gnomad4 OTH AF: 0.00568

Alfa AF: 0.00625 Hom.: 0

Bravo AF: 0.00541

Asia WGS AF: 0.000867 AC: 3 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	15
DANN	Benign	0.74

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: rs10508070; hg19: chr13-102286631;