NM_002214.3:c.960+3938A>G

Variant names:

• chr7-20385823-A-G
• rs2158250
• NM_002214.3:c.960+3938A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002214.3(ITGB8):​c.960+3938A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0995 in 152,244 control chromosomes in the GnomAD database, including 961 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 0.10 (961 hom., cov: 32)
• Consequence: ITGB8 NM_002214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.45

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB8	NM_002214.3	c.960+3938A>G		intron_variant	Intron 6 of 13	ENST00000222573.5	NP_002205.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB8	ENST00000222573.5	c.960+3938A>G		intron_variant	Intron 6 of 13	1	NM_002214.3	ENSP00000222573.3
ITGB8	ENST00000478974.1	n.1665+3938A>G		intron_variant	Intron 6 of 8	1
ITGB8	ENST00000537992.5	c.555+3938A>G		intron_variant	Intron 7 of 14	2		ENSP00000441561.1

Frequencies

GnomAD3 genomes AF: 0.0996 AC: 15148 AN: 152126 Hom.: 960 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.0723

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.0961

Gnomad FIN AF: 0.0919

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0787

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.0995 AC: 15151 AN: 152244 Hom.: 961 Cov.: 32 AF XY: 0.102 AC XY: 7618 AN XY: 74446

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.0724

Gnomad4 ASJ AF: 0.0899

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.0952

Gnomad4 FIN AF: 0.0919

Gnomad4 NFE AF: 0.0787

Gnomad4 OTH AF: 0.0919

Alfa AF: 0.0864 Hom.: 174

Bravo AF: 0.101

Asia WGS AF: 0.206 AC: 714 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.9
DANN	Benign	0.68

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: rs2158250; hg19: chr7-20425446;