rs2675

chr3-124763266-T-G

Variant summary

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

The NM_002213.5(ITGB5):c.*357A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 201,470 control chromosomes in the GnomAD database, including 3,288 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 0.17 (2418 hom., cov: 34)
  • Exomes 𝑓: 0.18 (870 hom.)
• Consequence: ITGB5 NM_002213.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

ITGB5 (HGNC:6160): (integrin subunit beta 5) This gene encodes a beta subunit of integrin, which can combine with different alpha chains to form a variety of integrin heterodimers. Integrins are integral cell-surface receptors that participate in cell adhesion as well as cell-surface mediated signaling. The alphav beta5 integrin is involved in adhesion to vitronectin. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGB5	NM_002213.5	c.*357A>C		3_prime_UTR_variant	15/15	ENST00000296181.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB5	ENST00000296181.9	c.*357A>C		3_prime_UTR_variant	15/15	1	NM_002213.5	P1
ITGB5	ENST00000460797.5	n.1910A>C		non_coding_transcript_exon_variant	4/4	2

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25785 AN: 152180 Hom.: 2416 Cov.: 34

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.0994

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.168

GnomAD4 exome AF: 0.176 AC: 8645 AN: 49172 Hom.: 870 Cov.: 0 AF XY: 0.177 AC XY: 4465 AN XY: 25288

Gnomad4 AFR exome AF: 0.116

Gnomad4 AMR exome AF: 0.271

Gnomad4 ASJ exome AF: 0.0965

Gnomad4 EAS exome AF: 0.192

Gnomad4 SAS exome AF: 0.216

Gnomad4 FIN exome AF: 0.185

Gnomad4 NFE exome AF: 0.168

Gnomad4 OTH exome AF: 0.155

GnomAD4 genome AF: 0.169 AC: 25797 AN: 152298 Hom.: 2418 Cov.: 34 AF XY: 0.172 AC XY: 12830 AN XY: 74470

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.0994

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.169

Alfa AF: 0.162 Hom.: 478

Bravo AF: 0.170

Asia WGS AF: 0.190 AC: 663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.17
Dann	Benign	0.45
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs2675; hg19: chr3-124482113;