dbSNP rs2675: ITGB5:c.*357A>C (chr3-124763266-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.39

Publications

18 publications found

Variant links:

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]

ITGB5 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB5	NM_002213.5 link	c.*357A>C		3_prime_UTR_variant	Exon 15 of 15	ENST00000296181.9	NP_002204.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB5	ENST00000296181.9 link	c.*357A>C		3_prime_UTR_variant	Exon 15 of 15	1	NM_002213.5	ENSP00000296181.4
ITGB5	ENST00000460797.5 link	n.1910A>C		non_coding_transcript_exon_variant	Exon 4 of 4	2

Frequencies

GnomAD3 genomes

AF:

0.169

AC:

25785

AN:

152180

Hom.:

2416

Cov.:

show subpopulations

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.:

AF XY:

0.177

AC XY:

4465

AN XY:

25288

show subpopulations

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:

AN:

206

European-Non Finnish (NFE)

AF:

0.168

AC:

5102

AN:

30398

Other (OTH)

AF:

0.155

AC:

449

AN:

2900

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

340

680

1019

1359

1699

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

164

246

328

410

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.169

AC:

25797

AN:

152298

Hom.:

2418

Cov.:

AF XY:

0.172

AC XY:

12830

AN XY:

74470

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.171

AC:

11619

AN:

68016

Other (OTH)

AF:

0.169

AC:

358

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1142

2284

3427

4569

5711

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

284

568

852

1136

1420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.17

(source)

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)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over