rs206198

Positions:

• chr7-20332135-G-A
• chr7-20332135-G-T

Variant summary

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

The NM_002214.3(ITGB8):​c.127+202G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 1,154,244 control chromosomes in the GnomAD database, including 119,613 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 0.52 (21936 hom., cov: 33)
  • Exomes 𝑓: 0.43 (97677 hom.)
• Consequence: ITGB8 NM_002214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGB8	NM_002214.3	c.127+202G>A		intron_variant		ENST00000222573.5	NP_002205.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB8	ENST00000222573.5	c.127+202G>A		intron_variant		1	NM_002214.3	ENSP00000222573	P1
ITGB8	ENST00000460204.1	n.47+112G>A		intron_variant, non_coding_transcript_variant		1
ITGB8	ENST00000478974.1	n.832+202G>A		intron_variant, non_coding_transcript_variant		1
ITGB8	ENST00000537992.5	c.-279+112G>A		intron_variant		2		ENSP00000441561

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78566 AN: 151968 Hom.: 21909 Cov.: 33

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.494

GnomAD4 exome AF: 0.431 AC: 432406 AN: 1002158 Hom.: 97677 AF XY: 0.435 AC XY: 214238 AN XY: 492396

Gnomad4 AFR exome AF: 0.716

Gnomad4 AMR exome AF: 0.630

Gnomad4 ASJ exome AF: 0.401

Gnomad4 EAS exome AF: 0.642

Gnomad4 SAS exome AF: 0.631

Gnomad4 FIN exome AF: 0.370

Gnomad4 NFE exome AF: 0.399

Gnomad4 OTH exome AF: 0.456

GnomAD4 genome AF: 0.517 AC: 78651 AN: 152086 Hom.: 21936 Cov.: 33 AF XY: 0.520 AC XY: 38655 AN XY: 74352

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.494

Alfa AF: 0.435 Hom.: 15211

Bravo AF: 0.537

Asia WGS AF: 0.655 AC: 2281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.0
DANN	Benign	0.74

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: rs206198; hg19: chr7-20371758;