ENST00000477859.1:n.5088C>G

Variant names:

• chr7-20381596-C-G
• rs2301727
• ENST00000477859.1:n.5088C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000477859.1(ITGB8):​n.5088C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 484,094 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000062 (0 hom.)
• Consequence: ITGB8 ENST00000477859.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB8	NM_002214.3	c.802-131C>G		intron_variant	Intron 5 of 13	ENST00000222573.5	NP_002205.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB8	ENST00000477859.1	n.5088C>G		non_coding_transcript_exon_variant	Exon 2 of 2	1
ITGB8	ENST00000222573.5	c.802-131C>G		intron_variant	Intron 5 of 13	1	NM_002214.3	ENSP00000222573.3
ITGB8	ENST00000478974.1	n.1507-131C>G		intron_variant	Intron 5 of 8	1
ITGB8	ENST00000537992.5	c.397-131C>G		intron_variant	Intron 6 of 14	2		ENSP00000441561.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000620 AC: 3 AN: 484094 Hom.: 0 Cov.: 6 AF XY: 0.00000786 AC XY: 2 AN XY: 254380

African (AFR) AF: 0.00 AC: 0 AN: 12734

American (AMR) AF: 0.00 AC: 0 AN: 19542

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14170

East Asian (EAS) AF: 0.00 AC: 0 AN: 31308

South Asian (SAS) AF: 0.00 AC: 0 AN: 41798

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34702

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2326

European-Non Finnish (NFE) AF: 0.00000999 AC: 3 AN: 300210

Other (OTH) AF: 0.00 AC: 0 AN: 27304

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.5
DANN	Benign	0.60
PhyloP100		-0.30

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: rs2301727; hg19: chr7-20421219;