13-101453980-C-A

Variant names:

• chr13-101453980-C-A
• rs1326478098
• NM_004791.3:c.196C>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.196C>A​(p.Arg66Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000722 in 1,385,650 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.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.2e-7 (0 hom.)
• Consequence: ITGBL1 NM_004791.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.45
• 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 (BayesDel_noAF=-0.26).
• BP7: Synonymous conserved (PhyloP=2.45 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.196C>A	p.Arg66Arg	synonymous	Exon 2 of 11	NP_004782.1	O95965-1
	ITGBL1	NM_001271755.2		c.196C>A	p.Arg66Arg	synonymous	Exon 2 of 10	NP_001258684.1	A0A087WY35
	ITGBL1	NM_001271754.2		c.-108+1049C>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.196C>A	p.Arg66Arg	synonymous	Exon 2 of 11	ENSP00000365351.3	O95965-1
	ITGBL1	ENST00000618057.4	TSL:1	c.196C>A	p.Arg66Arg	synonymous	Exon 2 of 10	ENSP00000481484.1	A0A087WY35
	ITGBL1	ENST00000907748.1		c.196C>A	p.Arg66Arg	synonymous	Exon 2 of 12	ENSP00000577807.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.22e-7 AC: 1 AN: 1385650 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 684196

African (AFR) AF: 0.00 AC: 0 AN: 30356

American (AMR) AF: 0.00 AC: 0 AN: 34416

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24696

East Asian (EAS) AF: 0.00 AC: 0 AN: 34702

South Asian (SAS) AF: 0.00 AC: 0 AN: 77056

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 48970

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5566

European-Non Finnish (NFE) AF: 9.32e-7 AC: 1 AN: 1072586

Other (OTH) AF: 0.00 AC: 0 AN: 57302

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	15
DANN	Benign	0.93
PhyloP100		2.4

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: rs1326478098; hg19: chr13-102106331;