rs3807936

chr7-20353029-T-Cchr7-20353029-T-G

Variant summary

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

The NM_002214.3(ITGB8):c.128-10608T>C variant causes a intron 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 NM_002214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231

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 = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGB8	NM_002214.3	c.128-10608T>C		intron_variant		ENST00000222573.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB8	ENST00000222573.5	c.128-10608T>C		intron_variant		1	NM_002214.3	P1
ITGB8	ENST00000460204.1	n.762T>C		non_coding_transcript_exon_variant	2/2	1
ITGB8	ENST00000478974.1	n.833-10608T>C		intron_variant, non_coding_transcript_variant		1
ITGB8	ENST00000537992.5	c.-278-10608T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16176 AN: 152110 Hom.: 1011 Cov.: 33

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: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.106 AC: 16184 AN: 152228 Hom.: 1014 Cov.: 33 AF XY: 0.109 AC XY: 8141 AN XY: 74446

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.0732

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.0958

Gnomad4 NFE AF: 0.0887

Gnomad4 OTH AF: 0.0980

Alfa AF: 0.0911 Hom.: 909

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
Dann	Benign	0.83

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: rs3807936; hg19: chr7-20392652;