Genetic Variant ITGB8:n.5088C>T (chr7-20381596-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000477859.1(ITGB8):n.5088C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 636,036 control chromosomes in the GnomAD database, including 5,166 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 0.10 ( 1043 hom., cov: 33)

Exomes 𝑓: 0.11 ( 4123 hom. )

Consequence

ITGB8
ENST00000477859.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.300

Publications

7 publications found

Variant links:

Genes affected

ITGB8 (HGNC:6163): (integrin subunit beta 8) This gene is a member of the integrin beta chain family and encodes a single-pass type I membrane protein with a VWFA domain and four cysteine-rich repeats. This protein noncovalently binds to an alpha subunit to form a heterodimeric integrin complex. In general, integrin complexes mediate cell-cell and cell-extracellular matrix interactions and this complex plays a role in human airway epithelial proliferation. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized. [provided by RefSeq, Jul 2008]

ITGB8 links:

Genome browser will be placed here

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=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB8	NM_002214.3 link	c.802-131C>T		intron_variant	Intron 5 of 13	ENST00000222573.5	NP_002205.1	P26012-1Q9BUG9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ITGB8	ENST00000477859.1 link	n.5088C>T	non_coding_transcript_exon_variant	Exon 2 of 2	1
ITGB8	ENST00000222573.5 link	c.802-131C>T	intron_variant	Intron 5 of 13	1	NM_002214.3	ENSP00000222573.3	P26012-1
ITGB8	ENST00000478974.1 link	n.1507-131C>T	intron_variant	Intron 5 of 8	1
ITGB8	ENST00000537992.5 link	c.397-131C>T	intron_variant	Intron 6 of 14	2		ENSP00000441561.1	P26012-2

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

15978

AN:

152152

Hom.:

1042

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.140

Gnomad AMR

AF:

0.0762

Gnomad ASJ

AF:

0.0922

Gnomad EAS

AF:

0.390

Gnomad SAS

AF:

0.109

Gnomad FIN

AF:

0.0975

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0872

Gnomad OTH

AF:

0.0984

GnomAD4 exome

AF:

0.108

AC:

52245

AN:

483766

Hom.:

4123

Cov.:

AF XY:

0.107

AC XY:

27092

AN XY:

254192

show subpopulations

African (AFR)

AF:

0.109

AC:

1393

AN:

12730

American (AMR)

AF:

0.0731

AC:

1428

AN:

19530

Ashkenazi Jewish (ASJ)

AF:

0.0817

AC:

1158

AN:

14166

East Asian (EAS)

AF:

0.373

AC:

11666

AN:

31258

South Asian (SAS)

AF:

0.0972

AC:

4060

AN:

41758

European-Finnish (FIN)

AF:

0.103

AC:

3572

AN:

34676

Middle Eastern (MID)

AF:

0.0780

AC:

181

AN:

2320

European-Non Finnish (NFE)

AF:

0.0861

AC:

25841

AN:

300042

Other (OTH)

AF:

0.108

AC:

2946

AN:

27286

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

2130

4261

6391

8522

10652

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

336

672

1008

1344

1680

<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:

0.105

AC:

15980

AN:

152270

Hom.:

1043

Cov.:

AF XY:

0.107

AC XY:

7995

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.112

AC:

4635

AN:

41562

American (AMR)

AF:

0.0762

AC:

1166

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0922

AC:

320

AN:

3472

East Asian (EAS)

AF:

0.390

AC:

2018

AN:

5178

South Asian (SAS)

AF:

0.108

AC:

523

AN:

4828

European-Finnish (FIN)

AF:

0.0975

AC:

1032

AN:

10586

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0872

AC:

5932

AN:

68024

Other (OTH)

AF:

0.0978

AC:

207

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

702

1405

2107

2810

3512

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

186

372

558

744

930

<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:

0.0938

Hom.:

492

Bravo

AF:

0.105

Asia WGS

AF:

0.210

AC:

728

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

7.2

(source)

DANN

Benign

0.84

PhyloP100

-0.30

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