7-20333792-T-A

Variant names:

• chr7-20333792-T-A
• rs11982847
• NM_002214.3:c.127+1859T>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_002214.3(ITGB8):​c.127+1859T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,088 control chromosomes in the GnomAD database, including 5,484 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 0.25 (5484 hom., cov: 33)
• Consequence: ITGB8 NM_002214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.92
• Publications: 3 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB8	NM_002214.3	c.127+1859T>A		intron_variant	Intron 1 of 13	ENST00000222573.5	NP_002205.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB8	ENST00000222573.5	c.127+1859T>A		intron_variant	Intron 1 of 13	1	NM_002214.3	ENSP00000222573.3
ITGB8	ENST00000460204.1	n.47+1769T>A		intron_variant	Intron 1 of 1	1
ITGB8	ENST00000478974.1	n.832+1859T>A		intron_variant	Intron 1 of 8	1
ITGB8	ENST00000537992.5	c.-279+1769T>A		intron_variant	Intron 2 of 14	2		ENSP00000441561.1

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38498 AN: 151970 Hom.: 5486 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.00577

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.253 AC: 38500 AN: 152088 Hom.: 5484 Cov.: 33 AF XY: 0.250 AC XY: 18617 AN XY: 74350

African (AFR) AF: 0.179 AC: 7411 AN: 41514

American (AMR) AF: 0.194 AC: 2961 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1173 AN: 3468

East Asian (EAS) AF: 0.00578 AC: 30 AN: 5190

South Asian (SAS) AF: 0.114 AC: 552 AN: 4830

European-Finnish (FIN) AF: 0.369 AC: 3906 AN: 10574

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21586 AN: 67898

Other (OTH) AF: 0.277 AC: 585 AN: 2112

Alfa AF: 0.193 Hom.: 480

Bravo AF: 0.235

Asia WGS AF: 0.0670 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	17
DANN	Benign	0.82
PhyloP100		1.9
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: rs11982847; hg19: chr7-20373415;