10-32908269-A-T

Variant names:

• chr10-32908269-A-T
• rs1316757
• NM_002211.4:c.2331+99T>A

Variant summary

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

The NM_002211.4(ITGB1):​c.2331+99T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000997 in 1,003,298 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 32)
  • Exomes 𝑓: 0.0000010 (0 hom.)
• Consequence: ITGB1 NM_002211.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 0 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]

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=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002211.4. 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.2331+99T>A		intron	N/A	NP_002202.2
	ITGB1	NM_033668.2		c.2331+99T>A		intron	N/A	NP_391988.1	P05556-5
	ITGB1	NM_133376.3		c.2331+99T>A		intron	N/A	NP_596867.1	P05556-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB1	ENST00000302278.8	TSL:1 MANE Select	c.2331+99T>A		intron	N/A	ENSP00000303351.3	P05556-1
	ITGB1	ENST00000488427.2	TSL:1	c.2160+99T>A		intron	N/A	ENSP00000417508.2	H7C4K3
	ITGB1	ENST00000676460.1		c.*60T>A		3_prime_UTR	Exon 15 of 15	ENSP00000504641.1	P05556-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 9.97e-7 AC: 1 AN: 1003298 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 515788

African (AFR) AF: 0.00 AC: 0 AN: 23918

American (AMR) AF: 0.00 AC: 0 AN: 39844

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22288

East Asian (EAS) AF: 0.00 AC: 0 AN: 37398

South Asian (SAS) AF: 0.00 AC: 0 AN: 72396

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52210

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4724

European-Non Finnish (NFE) AF: 0.00000142 AC: 1 AN: 705664

Other (OTH) AF: 0.00 AC: 0 AN: 44856

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.2
DANN	Benign	0.68
PhyloP100		0.098

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: rs1316757; hg19: chr10-33197197;