rs4798

chr2-9406676-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004763.5(ITGB1BP1):c.*158G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 636,988 control chromosomes in the GnomAD database, including 14,665 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 (5251 hom., cov: 33)
  • Exomes 𝑓: 0.18 (9414 hom.)
• Consequence: ITGB1BP1 NM_004763.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584

Genes affected

ITGB1BP1 (HGNC:23927): (integrin subunit beta 1 binding protein 1) The cytoplasmic domains of integrins are essential for cell adhesion. The protein encoded by this gene binds to the beta1 integrin cytoplasmic domain. The interaction between this protein and beta1 integrin is highly specific. Two isoforms of this protein are derived from alternatively spliced transcripts. The shorter form of this protein does not interact with the beta1 integrin cytoplasmic domain. The longer form is a phosphoprotein and the extent of its phosphorylation is regulated by the cell-matrix interaction, suggesting an important role of this protein during integrin-dependent cell adhesion. Several transcript variants, some protein-coding and some non-protein coding, have been found for this gene. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGB1BP1	NM_004763.5	c.*158G>A		3_prime_UTR_variant	7/7	ENST00000355346.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB1BP1	ENST00000355346.9	c.*158G>A		3_prime_UTR_variant	7/7	1	NM_004763.5	P1

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37030 AN: 152000 Hom.: 5237 Cov.: 33

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0243

Gnomad SAS AF: 0.0808

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.231

GnomAD4 exome AF: 0.183 AC: 88696 AN: 484870 Hom.: 9414 Cov.: 5 AF XY: 0.176 AC XY: 45276 AN XY: 256526

Gnomad4 AFR exome AF: 0.394

Gnomad4 AMR exome AF: 0.139

Gnomad4 ASJ exome AF: 0.225

Gnomad4 EAS exome AF: 0.0213

Gnomad4 SAS exome AF: 0.0804

Gnomad4 FIN exome AF: 0.171

Gnomad4 NFE exome AF: 0.208

Gnomad4 OTH exome AF: 0.205

GnomAD4 genome AF: 0.244 AC: 37071 AN: 152118 Hom.: 5251 Cov.: 33 AF XY: 0.237 AC XY: 17625 AN XY: 74384

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.0241

Gnomad4 SAS AF: 0.0809

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.228

Alfa AF: 0.209 Hom.: 1958

Bravo AF: 0.255

Asia WGS AF: 0.0910 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	4.0
Dann	Benign	0.85

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

Publications

LitVar

Other links and lift over

dbSNP: rs4798; hg19: chr2-9546805;