chr13-101454087-G-A

Variant names:

• chr13-101454087-G-A
• rs150532305
• NM_004791.3:c.303G>A

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_004791.3(ITGBL1):​c.303G>A​(p.Gly101Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000704 in 1,420,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G101G) has been classified as Benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.0e-7 (0 hom.)
• Consequence: ITGBL1 NM_004791.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.816
• 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: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.10436651).
• BP7: Synonymous conserved (PhyloP=-0.816 with no splicing effect.

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.303G>A	p.Gly101Gly	synonymous	Exon 2 of 11	NP_004782.1	O95965-1
	ITGBL1	NM_001271755.2		c.303G>A	p.Gly101Gly	synonymous	Exon 2 of 10	NP_001258684.1	A0A087WY35
	ITGBL1	NM_001271754.2		c.-108+1156G>A		intron	N/A	NP_001258683.1	O95965-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGBL1	ENST00000376180.8	TSL:1 MANE Select	c.303G>A	p.Gly101Gly	synonymous	Exon 2 of 11	ENSP00000365351.3	O95965-1
	ITGBL1	ENST00000618057.4	TSL:1	c.303G>A	p.Gly101Gly	synonymous	Exon 2 of 10	ENSP00000481484.1	A0A087WY35
	ITGBL1	ENST00000907748.1		c.303G>A	p.Gly101Gly	synonymous	Exon 2 of 12	ENSP00000577807.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.04e-7 AC: 1 AN: 1420856 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 703944

African (AFR) AF: 0.00 AC: 0 AN: 32216

American (AMR) AF: 0.00 AC: 0 AN: 39398

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25170

East Asian (EAS) AF: 0.00 AC: 0 AN: 37362

South Asian (SAS) AF: 0.00 AC: 0 AN: 79732

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51290

Middle Eastern (MID) AF: 0.000176 AC: 1 AN: 5684

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1091290

Other (OTH) AF: 0.00 AC: 0 AN: 58714

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.096
BayesDel_addAF	Benign	-0.34	T
BayesDel_noAF	Benign	-0.72
CADD	Benign	3.9
DANN	Benign	0.95
DEOGEN2	Benign	0.0064	T
Eigen	Benign	-0.68
Eigen_PC	Benign	-0.78
FATHMM_MKL	Benign	0.20	N
LIST_S2	Benign	0.25	T
MetaRNN	Benign	0.10	T
MetaSVM	Benign	-0.88	T
PhyloP100		-0.82
Sift4G	Benign	0.089	T
Vest4		0.20
MVP		0.15
ClinPred		0.78	D
GERP RS		-1.9

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: rs150532305; hg19: chr13-102106438;