chr7-20391962-C-T

Position:

• chr7-20391962-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.1056+464C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 151,930 control chromosomes in the GnomAD database, including 25,145 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 0.57 (25145 hom., cov: 31)
• Consequence: ITGB8 NM_002214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) 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.1056+464C>T		intron_variant		ENST00000222573.5	NP_002205.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB8	ENST00000222573.5	c.1056+464C>T		intron_variant		1	NM_002214.3	ENSP00000222573	P1
ITGB8	ENST00000478974.1	n.1761+464C>T		intron_variant, non_coding_transcript_variant		1
ITGB8	ENST00000537992.5	c.651+464C>T		intron_variant		2		ENSP00000441561

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86294 AN: 151812 Hom.: 25133 Cov.: 31

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.555

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.568 AC: 86353 AN: 151930 Hom.: 25145 Cov.: 31 AF XY: 0.569 AC XY: 42259 AN XY: 74244

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.553

Alfa AF: 0.536 Hom.: 3273

Bravo AF: 0.584

Asia WGS AF: 0.650 AC: 2266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.75

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: rs10231365; hg19: chr7-20431585;