7-20381596-C-T

Position:

• chr7-20381596-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002214.3(ITGB8):​c.802-131C>T variant causes a intron 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 NM_002214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ITGB8	NM_002214.3	c.802-131C>T		intron_variant		ENST00000222573.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB8	ENST00000222573.5	c.802-131C>T		intron_variant		1	NM_002214.3	P1
ITGB8	ENST00000477859.1	n.5088C>T		non_coding_transcript_exon_variant	2/2	1
ITGB8	ENST00000478974.1	n.1507-131C>T		intron_variant, non_coding_transcript_variant		1
ITGB8	ENST00000537992.5	c.397-131C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15978 AN: 152152 Hom.: 1042 Cov.: 33

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.: 6 AF XY: 0.107 AC XY: 27092 AN XY: 254192

Gnomad4 AFR exome AF: 0.109

Gnomad4 AMR exome AF: 0.0731

Gnomad4 ASJ exome AF: 0.0817

Gnomad4 EAS exome AF: 0.373

Gnomad4 SAS exome AF: 0.0972

Gnomad4 FIN exome AF: 0.103

Gnomad4 NFE exome AF: 0.0861

Gnomad4 OTH exome AF: 0.108

GnomAD4 genome AF: 0.105 AC: 15980 AN: 152270 Hom.: 1043 Cov.: 33 AF XY: 0.107 AC XY: 7995 AN XY: 74442

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.0762

Gnomad4 ASJ AF: 0.0922

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0975

Gnomad4 NFE AF: 0.0872

Gnomad4 OTH AF: 0.0978

Alfa AF: 0.0938 Hom.: 379

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
DANN	Benign	0.84

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

Other links and lift over

dbSNP: rs2301727; hg19: chr7-20421219;