3-124763266-T-G

Variant names:

• chr3-124763266-T-G
• rs2675
• NM_002213.5:c.*357A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002213.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB5	NM_002213.5	MANE Select	c.*357A>C		3_prime_UTR	Exon 15 of 15	NP_002204.2
	ITGB5	NM_001354764.2		c.*357A>C		3_prime_UTR	Exon 15 of 15	NP_001341693.1
	ITGB5	NM_001354765.1		c.*357A>C		3_prime_UTR	Exon 15 of 15	NP_001341694.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB5	ENST00000296181.9	TSL:1 MANE Select	c.*357A>C		3_prime_UTR	Exon 15 of 15	ENSP00000296181.4
	ITGB5	ENST00000460797.5	TSL:2	n.1910A>C		non_coding_transcript_exon	Exon 4 of 4

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

African (AFR) AF: 0.116 AC: 220 AN: 1894

American (AMR) AF: 0.271 AC: 879 AN: 3248

Ashkenazi Jewish (ASJ) AF: 0.0965 AC: 148 AN: 1534

East Asian (EAS) AF: 0.192 AC: 476 AN: 2480

South Asian (SAS) AF: 0.216 AC: 938 AN: 4344

European-Finnish (FIN) AF: 0.185 AC: 401 AN: 2168

Middle Eastern (MID) AF: 0.155 AC: 32 AN: 206

European-Non Finnish (NFE) AF: 0.168 AC: 5102 AN: 30398

Other (OTH) AF: 0.155 AC: 449 AN: 2900

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

African (AFR) AF: 0.129 AC: 5349 AN: 41560

American (AMR) AF: 0.253 AC: 3876 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0994 AC: 345 AN: 3472

East Asian (EAS) AF: 0.176 AC: 914 AN: 5188

South Asian (SAS) AF: 0.209 AC: 1007 AN: 4828

European-Finnish (FIN) AF: 0.201 AC: 2135 AN: 10608

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11619 AN: 68016

Other (OTH) AF: 0.169 AC: 358 AN: 2116

Alfa AF: 0.166 Hom.: 794

Bravo AF: 0.170

Asia WGS AF: 0.190 AC: 663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.17
DANN	Benign	0.45
PhyloP100		-1.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs2675; hg19: chr3-124482113;