13-101457534-A-G

Variant names:

• chr13-101457534-A-G
• rs9557656
• NM_004791.3:c.316+3434A>G

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+3434A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,288 control chromosomes in the GnomAD database, including 1,742 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 0.13 (1742 hom., cov: 32)
• Consequence: ITGBL1 NM_004791.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.666
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 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+3434A>G		intron	N/A	NP_004782.1
	ITGBL1	NM_001271755.2		c.316+3434A>G		intron	N/A	NP_001258684.1
	ITGBL1	NM_001271754.2		c.-108+4603A>G		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+3434A>G		intron	N/A	ENSP00000365351.3
	ITGBL1	ENST00000618057.4	TSL:1	c.316+3434A>G		intron	N/A	ENSP00000481484.1
	ITGBL1	ENST00000545560.6	TSL:2	c.-108+4603A>G		intron	N/A	ENSP00000439903.1

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20119 AN: 152170 Hom.: 1747 Cov.: 32

Gnomad AFR AF: 0.0622

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.132 AC: 20113 AN: 152288 Hom.: 1742 Cov.: 32 AF XY: 0.137 AC XY: 10182 AN XY: 74466

African (AFR) AF: 0.0620 AC: 2578 AN: 41570

American (AMR) AF: 0.238 AC: 3637 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 764 AN: 3468

East Asian (EAS) AF: 0.382 AC: 1977 AN: 5182

South Asian (SAS) AF: 0.195 AC: 942 AN: 4822

European-Finnish (FIN) AF: 0.121 AC: 1280 AN: 10610

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.125 AC: 8517 AN: 68022

Other (OTH) AF: 0.150 AC: 317 AN: 2114

Alfa AF: 0.122 Hom.: 666

Bravo AF: 0.142

Asia WGS AF: 0.283 AC: 981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.12
DANN	Benign	0.50
PhyloP100		-0.67
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: rs9557656; hg19: chr13-102109885;