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2-160101949-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_000888.5(ITGB6):​c.2269-115T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 638,084 control chromosomes in the GnomAD database, including 8,978 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.17 ( 2607 hom., cov: 33)
Exomes 𝑓: 0.15 ( 6371 hom. )

Consequence

ITGB6
NM_000888.5 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.200
Variant links:
Genes affected
ITGB6 (HGNC:6161): (integrin subunit beta 6) This gene encodes a protein that is a member of the integrin superfamily. Members of this family are adhesion receptors that function in signaling from the extracellular matrix to the cell. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. The encoded protein forms a dimer with an alpha v chain and this heterodimer can bind to ligands like fibronectin and transforming growth factor beta 1. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 2-160101949-A-T is Benign according to our data. Variant chr2-160101949-A-T is described in ClinVar as [Benign]. Clinvar id is 1221702.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ITGB6NM_000888.5 linkuse as main transcriptc.2269-115T>A intron_variant ENST00000283249.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ITGB6ENST00000283249.7 linkuse as main transcriptc.2269-115T>A intron_variant 1 NM_000888.5 P1P18564-1

Frequencies

GnomAD3 genomes
AF:
0.174
AC:
26434
AN:
152020
Hom.:
2589
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.196
Gnomad AMI
AF:
0.0779
Gnomad AMR
AF:
0.306
Gnomad ASJ
AF:
0.148
Gnomad EAS
AF:
0.165
Gnomad SAS
AF:
0.127
Gnomad FIN
AF:
0.0975
Gnomad MID
AF:
0.0860
Gnomad NFE
AF:
0.149
Gnomad OTH
AF:
0.188
GnomAD4 exome
AF:
0.152
AC:
73941
AN:
485950
Hom.:
6371
AF XY:
0.149
AC XY:
38899
AN XY:
261216
show subpopulations
Gnomad4 AFR exome
AF:
0.196
Gnomad4 AMR exome
AF:
0.375
Gnomad4 ASJ exome
AF:
0.142
Gnomad4 EAS exome
AF:
0.163
Gnomad4 SAS exome
AF:
0.118
Gnomad4 FIN exome
AF:
0.110
Gnomad4 NFE exome
AF:
0.146
Gnomad4 OTH exome
AF:
0.164
GnomAD4 genome
AF:
0.174
AC:
26483
AN:
152134
Hom.:
2607
Cov.:
33
AF XY:
0.173
AC XY:
12874
AN XY:
74380
show subpopulations
Gnomad4 AFR
AF:
0.196
Gnomad4 AMR
AF:
0.307
Gnomad4 ASJ
AF:
0.148
Gnomad4 EAS
AF:
0.165
Gnomad4 SAS
AF:
0.127
Gnomad4 FIN
AF:
0.0975
Gnomad4 NFE
AF:
0.149
Gnomad4 OTH
AF:
0.187
Alfa
AF:
0.161
Hom.:
265
Bravo
AF:
0.194
Asia WGS
AF:
0.155
AC:
540
AN:
3476

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 19, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
2.7
DANN
Benign
0.43

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4078235; hg19: chr2-160958460; API