chr10-32901357-G-T

Variant names:

• chr10-32901357-G-T
• rs17468
• NM_002211.4:c.*213C>A

Variant summary

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

The NM_033668.2(ITGB1):​c.*285C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 22)
  • Exomes 𝑓: 0.0000033 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ITGB1 NM_033668.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.837
• Publications: 14 publications found

Genes affected

ITGB1 (HGNC:6153): (integrin subunit beta 1) Integrins are heterodimeric proteins made up of alpha and beta subunits. At least 18 alpha and 8 beta subunits have been described in mammals. Integrin family members are membrane receptors involved in cell adhesion and recognition in a variety of processes including embryogenesis, hemostasis, tissue repair, immune response and metastatic diffusion of tumor cells. This gene encodes a beta subunit. Multiple alternatively spliced transcript variants which encode different protein isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

SNORA86 (HGNC:50390): (small nucleolar RNA, H/ACA box 86)

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=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033668.2. 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
	ITGB1	NM_002211.4	MANE Select	c.*213C>A		3_prime_UTR	Exon 16 of 16	NP_002202.2
	ITGB1	NM_033668.2		c.*285C>A		3_prime_UTR	Exon 16 of 16	NP_391988.1
	ITGB1	NM_133376.3		c.*213C>A		3_prime_UTR	Exon 16 of 16	NP_596867.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB1	ENST00000302278.8	TSL:1 MANE Select	c.*213C>A		3_prime_UTR	Exon 16 of 16	ENSP00000303351.3
	ITGB1	ENST00000488427.2	TSL:1	c.*213C>A		3_prime_UTR	Exon 16 of 16	ENSP00000417508.2
	ITGB1	ENST00000966597.1		c.*213C>A		3_prime_UTR	Exon 17 of 17	ENSP00000636656.1

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000329 AC: 1 AN: 304110 Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0 AN XY: 157404

African (AFR) AF: 0.00 AC: 0 AN: 7514

American (AMR) AF: 0.00 AC: 0 AN: 8534

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9750

East Asian (EAS) AF: 0.00 AC: 0 AN: 22768

South Asian (SAS) AF: 0.00 AC: 0 AN: 14862

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 36394

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1420

European-Non Finnish (NFE) AF: 0.00000542 AC: 1 AN: 184588

Other (OTH) AF: 0.00 AC: 0 AN: 18280

GnomAD4 genome Cov.: 22

Alfa AF: 0.00 Hom.: 1807

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.70
PhyloP100		0.84

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: rs17468; hg19: chr10-33190285;