NM_004791.3:c.316+33085C>T

Variant names:

• chr13-101487185-C-T
• rs10851132
• NM_004791.3:c.316+33085C>T

Variant summary

Our verdict is Benign. The variant received -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
• 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 -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGBL1	NM_004791.3	MANE Select	c.316+33085C>T		intron	N/A	NP_004782.1
	ITGBL1	NM_001271755.2		c.316+33085C>T		intron	N/A	NP_001258684.1
	ITGBL1	NM_001271754.2		c.-108+34254C>T		intron	N/A	NP_001258683.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGBL1	ENST00000376180.8	TSL:1 MANE Select	c.316+33085C>T		intron	N/A	ENSP00000365351.3
	ITGBL1	ENST00000618057.4	TSL:1	c.316+33085C>T		intron	N/A	ENSP00000481484.1
	ITGBL1	ENST00000545560.6	TSL:2	c.-108+34254C>T		intron	N/A	ENSP00000439903.1

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

African (AFR) AF: 0.294 AC: 12197 AN: 41440

American (AMR) AF: 0.306 AC: 4669 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1127 AN: 3466

East Asian (EAS) AF: 0.477 AC: 2452 AN: 5140

South Asian (SAS) AF: 0.334 AC: 1609 AN: 4818

European-Finnish (FIN) AF: 0.159 AC: 1676 AN: 10570

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12179 AN: 67984

Other (OTH) AF: 0.257 AC: 544 AN: 2114

Alfa AF: 0.204 Hom.: 1807

Bravo AF: 0.258

Asia WGS AF: 0.423 AC: 1467 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.49
PhyloP100		-0.22
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: rs10851132; hg19: chr13-102139536; COSMIC: COSV107494656; COSMIC: COSV107494656;