rs4798

Variant names:

• chr2-9406676-C-T
• rs4798
• NM_004763.5:c.*158G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004763.5. 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
	ITGB1BP1	NM_004763.5	MANE Select	c.*158G>A		3_prime_UTR	Exon 7 of 7	NP_004754.1	O14713-1
	ITGB1BP1	NM_001319066.2		c.*158G>A		3_prime_UTR	Exon 7 of 7	NP_001305995.1	O14713-1
	ITGB1BP1	NM_001319067.2		c.*158G>A		3_prime_UTR	Exon 7 of 7	NP_001305996.1	O14713-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB1BP1	ENST00000355346.9	TSL:1 MANE Select	c.*158G>A		3_prime_UTR	Exon 7 of 7	ENSP00000347504.4	O14713-1
	ITGB1BP1	ENST00000464228.5	TSL:1	n.*565G>A		non_coding_transcript_exon	Exon 6 of 6	ENSP00000419452.1	F8WF20
	ITGB1BP1	ENST00000464228.5	TSL:1	n.*565G>A		3_prime_UTR	Exon 6 of 6	ENSP00000419452.1	F8WF20

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

African (AFR) AF: 0.394 AC: 5236 AN: 13304

American (AMR) AF: 0.139 AC: 3361 AN: 24180

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 3369 AN: 14976

East Asian (EAS) AF: 0.0213 AC: 664 AN: 31228

South Asian (SAS) AF: 0.0804 AC: 3866 AN: 48062

European-Finnish (FIN) AF: 0.171 AC: 6771 AN: 39544

Middle Eastern (MID) AF: 0.321 AC: 1105 AN: 3444

European-Non Finnish (NFE) AF: 0.208 AC: 58739 AN: 282842

Other (OTH) AF: 0.205 AC: 5585 AN: 27290

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

African (AFR) AF: 0.395 AC: 16381 AN: 41452

American (AMR) AF: 0.176 AC: 2698 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 780 AN: 3468

East Asian (EAS) AF: 0.0241 AC: 125 AN: 5182

South Asian (SAS) AF: 0.0809 AC: 390 AN: 4822

European-Finnish (FIN) AF: 0.162 AC: 1717 AN: 10580

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14037 AN: 68008

Other (OTH) AF: 0.228 AC: 481 AN: 2114

Alfa AF: 0.211 Hom.: 2646

Bravo AF: 0.255

Asia WGS AF: 0.0910 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	4.0
DANN	Benign	0.85
PhyloP100		-0.58
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: rs4798; hg19: chr2-9546805;