rs10239099

Variant names:

• chr7-20369251-G-C
• rs10239099
• NM_002214.3:c.388+2065G>C

Your query was ambiguous. Multiple possible variants found:

• chr7-20369251-G-C
• chr7-20369251-G-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.388+2065G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 151,936 control chromosomes in the GnomAD database, including 5,941 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 0.27 (5941 hom., cov: 32)
• Consequence: ITGB8 NM_002214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB8	NM_002214.3	c.388+2065G>C		intron_variant	Intron 3 of 13	ENST00000222573.5	NP_002205.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB8	ENST00000222573.5	c.388+2065G>C		intron_variant	Intron 3 of 13	1	NM_002214.3	ENSP00000222573.3
ITGB8	ENST00000477859.1	n.2542+2065G>C		intron_variant	Intron 1 of 1	1
ITGB8	ENST00000478974.1	n.1093+2065G>C		intron_variant	Intron 3 of 8	1
ITGB8	ENST00000537992.5	c.-18+2065G>C		intron_variant	Intron 4 of 14	2		ENSP00000441561.1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40370 AN: 151818 Hom.: 5940 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.266 AC: 40382 AN: 151936 Hom.: 5941 Cov.: 32 AF XY: 0.263 AC XY: 19553 AN XY: 74266

African (AFR) AF: 0.218 AC: 9027 AN: 41408

American (AMR) AF: 0.198 AC: 3018 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1104 AN: 3468

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5190

South Asian (SAS) AF: 0.117 AC: 565 AN: 4826

European-Finnish (FIN) AF: 0.371 AC: 3904 AN: 10530

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.321 AC: 21843 AN: 67946

Other (OTH) AF: 0.287 AC: 604 AN: 2108

Alfa AF: 0.182 Hom.: 440

Bravo AF: 0.250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.5
DANN	Benign	0.51
PhyloP100		0.076
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: rs10239099; hg19: chr7-20408874;