10-32901357-G-A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_033668.2(ITGB1):​c.*285C>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. There is a variant allele frequency bias in the population database for this variant (GnomAd4), which may indicate mosaicism or somatic mutations in the reference population data. 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_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 -4 ACMG points.

• 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>T		3_prime_UTR	Exon 16 of 16	NP_002202.2
	ITGB1	NM_033668.2		c.*285C>T		3_prime_UTR	Exon 16 of 16	NP_391988.1
	ITGB1	NM_133376.3		c.*213C>T		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>T		3_prime_UTR	Exon 16 of 16	ENSP00000303351.3
	ITGB1	ENST00000488427.2	TSL:1	c.*213C>T		3_prime_UTR	Exon 16 of 16	ENSP00000417508.2
	ITGB1	ENST00000966597.1		c.*213C>T		3_prime_UTR	Exon 17 of 17	ENSP00000636656.1

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

African (AFR) AF: 0.674 AC: 5049 AN: 7494

American (AMR) AF: 0.885 AC: 7540 AN: 8522

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 8763 AN: 9734

East Asian (EAS) AF: 0.688 AC: 15625 AN: 22704

South Asian (SAS) AF: 0.857 AC: 12710 AN: 14826

European-Finnish (FIN) AF: 0.872 AC: 31655 AN: 36322

Middle Eastern (MID) AF: 0.852 AC: 1205 AN: 1414

European-Non Finnish (NFE) AF: 0.891 AC: 164196 AN: 184294

Other (OTH) AF: 0.865 AC: 15772 AN: 18230

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.672 AC: 26657 AN: 39678

American (AMR) AF: 0.872 AC: 12707 AN: 14572

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3123 AN: 3432

East Asian (EAS) AF: 0.668 AC: 3323 AN: 4978

South Asian (SAS) AF: 0.862 AC: 3851 AN: 4466

European-Finnish (FIN) AF: 0.875 AC: 8637 AN: 9866

Middle Eastern (MID) AF: 0.868 AC: 250 AN: 288

European-Non Finnish (NFE) AF: 0.897 AC: 59933 AN: 66786

Other (OTH) AF: 0.837 AC: 1675 AN: 2002

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.827 Hom.: 1807

Bravo AF: 0.817

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	0.62
PhyloP100		0.84
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs17468; hg19: chr10-33190285; COSMIC: COSV56483704; COSMIC: COSV56483704;