chr10-33078876-C-G

Position:

• chr10-33078876-C-G

Variant summary

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

The NR_160030.1(IATPR):​n.338-3893G>C variant causes a intron, non coding transcript 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: IATPR NR_160030.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IATPR	NR_160030.1	n.338-3893G>C		intron_variant, non_coding_transcript_variant
ITGB1-DT	NR_184020.1	n.271-2466C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB1-DT	ENST00000450890.5	n.288-2466C>G		intron_variant, non_coding_transcript_variant		3
IATPR	ENST00000688819.2	n.320-3893G>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.801

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.569

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2666275; hg19: chr10-33367804;