chr2-9405901-C-T

Position:

• chr2-9405901-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.*933G>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 0.808 in 152,194 control chromosomes in the GnomAD database, including 50,607 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 0.81 (50606 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: ITGB1BP1 NM_004763.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970

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]

ITGB1BP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGB1BP1	NM_004763.5	c.*933G>A		3_prime_UTR_variant	7/7	ENST00000355346.9	NP_004754.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB1BP1	ENST00000355346	c.*933G>A		3_prime_UTR_variant	7/7	1	NM_004763.5	ENSP00000347504.4

Frequencies

GnomAD3 genomes AF: 0.809 AC: 122976 AN: 152064 Hom.: 50588 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.820

GnomAD4 exome AF: 0.500 AC: 6 AN: 12 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 5 AN XY: 10

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.375

GnomAD4 genome AF: 0.809 AC: 123042 AN: 152182 Hom.: 50606 Cov.: 32 AF XY: 0.812 AC XY: 60392 AN XY: 74388

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.849

Gnomad4 EAS AF: 0.852

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.924

Gnomad4 NFE AF: 0.872

Gnomad4 OTH AF: 0.815

Alfa AF: 0.861 Hom.: 72683

Bravo AF: 0.797

Asia WGS AF: 0.787 AC: 2733 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.55

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: rs10593; hg19: chr2-9546030;