dbSNP rs3807936: ITGB8:n.762T>C (chr7-20353029-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000460204.1(ITGB8):n.762T>C 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 0.106 in 152,232 control chromosomes in the GnomAD database, including 1,014 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 0.11 ( 1014 hom., cov: 33)

Exomes 𝑓: 0.25 ( 0 hom. )

Consequence

ITGB8
ENST00000460204.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.231

Publications

4 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 = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB8	NM_002214.3 link	c.128-10608T>C		intron_variant	Intron 1 of 13	ENST00000222573.5	NP_002205.1	P26012-1Q9BUG9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ITGB8	ENST00000460204.1 link	n.762T>C	non_coding_transcript_exon_variant	Exon 2 of 2	1
ITGB8	ENST00000222573.5 link	c.128-10608T>C	intron_variant	Intron 1 of 13	1	NM_002214.3	ENSP00000222573.3	P26012-1
ITGB8	ENST00000478974.1 link	n.833-10608T>C	intron_variant	Intron 1 of 8	1
ITGB8	ENST00000537992.5 link	c.-278-10608T>C	intron_variant	Intron 2 of 14	2		ENSP00000441561.1	P26012-2

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16176

AN:

152110

Hom.:

1011

Cov.:

show subpopulations

Gnomad AFR

AF:

0.118

Gnomad AMI

AF:

0.169

Gnomad AMR

AF:

0.0731

Gnomad ASJ

AF:

0.105

Gnomad EAS

AF:

0.368

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.0958

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0887

Gnomad OTH

AF:

0.0981

GnomAD4 exome

AF:

0.250

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.106

AC:

16184

AN:

152228

Hom.:

1014

Cov.:

AF XY:

0.109

AC XY:

8141

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.118

AC:

4889

AN:

41524

American (AMR)

AF:

0.0732

AC:

1120

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.105

AC:

364

AN:

3470

East Asian (EAS)

AF:

0.367

AC:

1897

AN:

5164

South Asian (SAS)

AF:

0.100

AC:

483

AN:

4828

European-Finnish (FIN)

AF:

0.0958

AC:

1016

AN:

10610

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0887

AC:

6030

AN:

68008

Other (OTH)

AF:

0.0980

AC:

207

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

754

1509

2263

3018

3772

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

194

388

582

776

970

<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:

0.0917

Hom.:

1169

Bravo

AF:

0.109

Asia WGS

AF:

0.208

AC:

719

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

4.6

(source)

DANN

Benign

0.83

PhyloP100

0.23

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