10-33075931-G-T

Variant names:

• chr10-33075931-G-T
• rs2666279
• ENST00000414157.3:n.280-5411G>T

Variant summary

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

The ENST00000414157.3(ITGB1-DT):​n.280-5411G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 152,002 control chromosomes in the GnomAD database, including 28,002 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 (28002 hom., cov: 31)
• Consequence: ITGB1-DT ENST00000414157.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IATPR	NR_160030.1		n.338-948C>A		intron	N/A
	ITGB1-DT	NR_184020.1		n.271-5411G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB1-DT	ENST00000414157.3	TSL:1	n.280-5411G>T		intron	N/A
	ITGB1-DT	ENST00000450890.6	TSL:3	n.621-5411G>T		intron	N/A
	ITGB1-DT	ENST00000666298.2		n.784-5411G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88229 AN: 151884 Hom.: 27937 Cov.: 31

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.581 AC: 88357 AN: 152002 Hom.: 28002 Cov.: 31 AF XY: 0.582 AC XY: 43266 AN XY: 74302

African (AFR) AF: 0.839 AC: 34806 AN: 41482

American (AMR) AF: 0.525 AC: 8015 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1832 AN: 3468

East Asian (EAS) AF: 0.800 AC: 4124 AN: 5154

South Asian (SAS) AF: 0.596 AC: 2867 AN: 4810

European-Finnish (FIN) AF: 0.442 AC: 4666 AN: 10566

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

European-Non Finnish (NFE) AF: 0.447 AC: 30341 AN: 67944

Other (OTH) AF: 0.573 AC: 1206 AN: 2106

Alfa AF: 0.435 Hom.: 2204

Bravo AF: 0.597

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.39
DANN	Benign	0.55
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs2666279; hg19: chr10-33364859;