chr13-101575144-A-T

Variant names:

• chr13-101575144-A-T
• rs9557704
• NM_004791.3:c.464-280A>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.464-280A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,914 control chromosomes in the GnomAD database, including 5,585 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 0.25 (5585 hom., cov: 32)
• Consequence: ITGBL1 NM_004791.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 6 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGBL1	NM_004791.3	c.464-280A>T		intron_variant	Intron 3 of 10	ENST00000376180.8	NP_004782.1
ITGBL1	NM_001271755.2	c.317-280A>T		intron_variant	Intron 2 of 9		NP_001258684.1
ITGBL1	NM_001271756.2	c.185-280A>T		intron_variant	Intron 2 of 9		NP_001258685.1
ITGBL1	NM_001271754.2	c.41-280A>T		intron_variant	Intron 2 of 10		NP_001258683.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGBL1	ENST00000376180.8	c.464-280A>T		intron_variant	Intron 3 of 10	1	NM_004791.3	ENSP00000365351.3
ITGBL1	ENST00000618057.4	c.317-280A>T		intron_variant	Intron 2 of 9	1		ENSP00000481484.1
ITGBL1	ENST00000376162.7	c.185-280A>T		intron_variant	Intron 2 of 9	2		ENSP00000365332.3
ITGBL1	ENST00000545560.6	c.41-280A>T		intron_variant	Intron 2 of 10	2		ENSP00000439903.1

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38375 AN: 151796 Hom.: 5586 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.253 AC: 38364 AN: 151914 Hom.: 5585 Cov.: 32 AF XY: 0.254 AC XY: 18884 AN XY: 74222

African (AFR) AF: 0.110 AC: 4578 AN: 41482

American (AMR) AF: 0.292 AC: 4447 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1378 AN: 3468

East Asian (EAS) AF: 0.461 AC: 2373 AN: 5148

South Asian (SAS) AF: 0.360 AC: 1735 AN: 4820

European-Finnish (FIN) AF: 0.287 AC: 3020 AN: 10540

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19938 AN: 67922

Other (OTH) AF: 0.281 AC: 594 AN: 2114

Alfa AF: 0.135 Hom.: 259

Bravo AF: 0.253

Asia WGS AF: 0.391 AC: 1359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.5
DANN	Benign	0.36
PhyloP100		1.1
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: rs9557704; hg19: chr13-102227495;