rs10231365

Variant names:

• chr7-20391962-C-T
• rs10231365
• NM_002214.3:c.1056+464C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002214.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB8	NM_002214.3	MANE Select	c.1056+464C>T		intron	N/A	NP_002205.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB8	ENST00000222573.5	TSL:1 MANE Select	c.1056+464C>T		intron	N/A	ENSP00000222573.3
	ITGB8	ENST00000478974.1	TSL:1	n.1761+464C>T		intron	N/A
	ITGB8	ENST00000537992.5	TSL:2	c.651+464C>T		intron	N/A	ENSP00000441561.1

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

African (AFR) AF: 0.660 AC: 27353 AN: 41418

American (AMR) AF: 0.651 AC: 9941 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1966 AN: 3468

East Asian (EAS) AF: 0.588 AC: 3035 AN: 5162

South Asian (SAS) AF: 0.723 AC: 3480 AN: 4810

European-Finnish (FIN) AF: 0.449 AC: 4724 AN: 10526

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34089 AN: 67962

Other (OTH) AF: 0.553 AC: 1165 AN: 2106

Alfa AF: 0.540 Hom.: 3455

Bravo AF: 0.584

Asia WGS AF: 0.650 AC: 2266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.75
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10231365; hg19: chr7-20431585;