rs10508070

Variant names:

• chr13-101634281-G-A
• rs10508070
• NM_004791.3:c.1015+35982G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004791.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGBL1	NM_004791.3	MANE Select	c.1015+35982G>A		intron	N/A	NP_004782.1	O95965-1
	ITGBL1	NM_001271755.2		c.868+35982G>A		intron	N/A	NP_001258684.1	A0A087WY35
	ITGBL1	NM_001271756.2		c.736+35982G>A		intron	N/A	NP_001258685.1	O95965-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGBL1	ENST00000376180.8	TSL:1 MANE Select	c.1015+35982G>A		intron	N/A	ENSP00000365351.3	O95965-1
	ITGBL1	ENST00000618057.4	TSL:1	c.868+35982G>A		intron	N/A	ENSP00000481484.1	A0A087WY35
	ITGBL1	ENST00000907748.1		c.1015+35982G>A		intron	N/A	ENSP00000577807.1

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

African (AFR) AF: 0.00168 AC: 70 AN: 41562

American (AMR) AF: 0.00360 AC: 55 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0277 AC: 96 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4824

European-Finnish (FIN) AF: 0.00226 AC: 24 AN: 10614

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00825 AC: 561 AN: 68012

Other (OTH) AF: 0.00568 AC: 12 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	15
DANN	Benign	0.74
PhyloP100		1.1

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: rs10508070; hg19: chr13-102286631;