rs62456081

Variant names:

• chr7-20330600-G-A
• rs62456081
• XM_011515394.3:c.36G>A

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The XM_011515394.3(ITGB8):​c.36G>A​(p.Lys12Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0583 in 152,404 control chromosomes in the GnomAD database, including 332 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 0.058 (332 hom., cov: 32)
  • Exomes 𝑓: 0.039 (0 hom.)
• Consequence: ITGB8 XM_011515394.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 1 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]

ITGB8-AS1 (HGNC:55257): (ITGB8 antisense RNA 1)

ENSG00000302794 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP7: Synonymous conserved (PhyloP=0.085 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0835 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789462.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB8-AS1	NR_110119.1		n.114-818C>T		intron	N/A
	ITGB8-AS1	NR_110120.1		n.113+1050C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB8-AS1	ENST00000789462.1		n.582C>T		non_coding_transcript_exon	Exon 1 of 1
	ITGB8-AS1	ENST00000789467.1		n.591C>T		non_coding_transcript_exon	Exon 1 of 3
	ITGB8-AS1	ENST00000789473.1		n.65C>T		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0584 AC: 8879 AN: 152114 Hom.: 333 Cov.: 32

Gnomad AFR AF: 0.0174

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0671

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.0768

Gnomad SAS AF: 0.0157

Gnomad FIN AF: 0.0523

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0854

Gnomad OTH AF: 0.0585

GnomAD4 exome AF: 0.0393 AC: 7 AN: 178 Hom.: 0 AF XY: 0.0352 AC XY: 5 AN XY: 142

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.250 AC: 1 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0417 AC: 6 AN: 144

Other (OTH) AF: 0.00 AC: 0 AN: 18

GnomAD4 genome AF: 0.0583 AC: 8882 AN: 152226 Hom.: 332 Cov.: 32 AF XY: 0.0548 AC XY: 4081 AN XY: 74450

African (AFR) AF: 0.0174 AC: 721 AN: 41554

American (AMR) AF: 0.0669 AC: 1024 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0369 AC: 128 AN: 3470

East Asian (EAS) AF: 0.0768 AC: 397 AN: 5168

South Asian (SAS) AF: 0.0159 AC: 77 AN: 4828

European-Finnish (FIN) AF: 0.0523 AC: 555 AN: 10620

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0854 AC: 5803 AN: 67968

Other (OTH) AF: 0.0598 AC: 126 AN: 2108

Alfa AF: 0.0732 Hom.: 688

Bravo AF: 0.0604

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.0
DANN	Benign	0.91
PhyloP100		0.085
PromoterAI		0.18	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs62456081; hg19: chr7-20370223;