10-33078876-C-G

Variant names:

• chr10-33078876-C-G
• rs2666275
• ENST00000414157.3:n.280-2466C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000414157.3(ITGB1-DT):​n.280-2466C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 151,994 control chromosomes in the GnomAD database, including 27,643 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 0.58 (27643 hom., cov: 31)
• Consequence: ITGB1-DT ENST00000414157.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• Publications: 1 publications found

Genes affected

ITGB1-DT (HGNC:53718): (ITGB1 divergent transcript)

IATPR (HGNC:53719): (ITGB1 adjacent tumor promoting lncRNA)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414157.3. 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
	IATPR	NR_160030.1		n.338-3893G>C		intron	N/A
	ITGB1-DT	NR_184020.1		n.271-2466C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB1-DT	ENST00000414157.3	TSL:1	n.280-2466C>G		intron	N/A
	ITGB1-DT	ENST00000450890.6	TSL:3	n.621-2466C>G		intron	N/A
	ITGB1-DT	ENST00000666298.2		n.784-2466C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87516 AN: 151874 Hom.: 27577 Cov.: 31

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.577 AC: 87645 AN: 151994 Hom.: 27643 Cov.: 31 AF XY: 0.577 AC XY: 42889 AN XY: 74276

African (AFR) AF: 0.836 AC: 34704 AN: 41494

American (AMR) AF: 0.523 AC: 7986 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1828 AN: 3468

East Asian (EAS) AF: 0.801 AC: 4142 AN: 5170

South Asian (SAS) AF: 0.596 AC: 2874 AN: 4820

European-Finnish (FIN) AF: 0.431 AC: 4539 AN: 10532

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29896 AN: 67928

Other (OTH) AF: 0.569 AC: 1200 AN: 2108

Alfa AF: 0.359 Hom.: 950

Bravo AF: 0.593

Asia WGS AF: 0.710 AC: 2468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.46
DANN	Benign	0.59
PhyloP100		-2.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2666275; hg19: chr10-33367804;