rs17468

Positions:

• chr10-32901357-G-A
• chr10-32901357-G-T

Variant summary

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

The NM_002211.4(ITGB1):​c.*213C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 146,962 control chromosomes in the GnomAD database, including 50,641 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 0.82 (50641 hom., cov: 22)
  • Exomes 𝑓: 0.86 (114130 hom.)
  • Failed GnomAD Quality Control
• Consequence: ITGB1 NM_002211.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.837

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGB1	NM_002211.4	c.*213C>T		3_prime_UTR_variant	16/16	ENST00000302278.8	NP_002202.2
SNORA86	NR_132768.1	n.116C>T		non_coding_transcript_exon_variant	1/1
ITGB1	NM_033668.2	c.*285C>T		3_prime_UTR_variant	16/16		NP_391988.1
ITGB1	NM_133376.3	c.*213C>T		3_prime_UTR_variant	16/16		NP_596867.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB1	ENST00000302278.8	c.*213C>T		3_prime_UTR_variant	16/16	1	NM_002211.4	ENSP00000303351	P4

Frequencies

GnomAD3 genomes AF: 0.823 AC: 120925 AN: 146844 Hom.: 50604 Cov.: 22

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.960

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.874

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.834

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.865 AC: 262515 AN: 303540 Hom.: 114130 Cov.: 3 AF XY: 0.866 AC XY: 136035 AN XY: 157104

Gnomad4 AFR exome AF: 0.674

Gnomad4 AMR exome AF: 0.885

Gnomad4 ASJ exome AF: 0.900

Gnomad4 EAS exome AF: 0.688

Gnomad4 SAS exome AF: 0.857

Gnomad4 FIN exome AF: 0.872

Gnomad4 NFE exome AF: 0.891

Gnomad4 OTH exome AF: 0.865

GnomAD4 genome AF: 0.823 AC: 121014 AN: 146962 Hom.: 50641 Cov.: 22 AF XY: 0.821 AC XY: 58678 AN XY: 71458

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.872

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.862

Gnomad4 FIN AF: 0.875

Gnomad4 NFE AF: 0.897

Gnomad4 OTH AF: 0.837

Alfa AF: 0.827 Hom.: 1807

Bravo AF: 0.817

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.62
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs17468; hg19: chr10-33190285; COSMIC: COSV56483704; COSMIC: COSV56483704;