10-33075931-G-T

Variant names:

• chr10-33075931-G-T
• rs2666279
• ENST00000414157.2:n.276-5411G>T

Variant summary

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

The ENST00000414157.2(ITGB1-DT):​n.276-5411G>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 ENST00000414157.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IATPR	NR_160030.1	n.338-948C>A		intron_variant	Intron 1 of 2
ITGB1-DT	NR_184020.1	n.271-5411G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB1-DT	ENST00000414157.2	n.276-5411G>T		intron_variant	Intron 2 of 2	1
ITGB1-DT	ENST00000450890.5	n.288-5411G>T		intron_variant	Intron 3 of 3	3
ITGB1-DT	ENST00000666298.1	n.342-5411G>T		intron_variant	Intron 3 of 3

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

Gnomad4 AFR AF: 0.839

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.800

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.573

Alfa AF: 0.419 Hom.: 1945

Bravo AF: 0.597

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2666279; hg19: chr10-33364859;