rs11009218

Positions:

• chr10-33082032-C-T

Variant summary

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

The NR_184020.1(ITGB1-DT):​n.961C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,176 control chromosomes in the GnomAD database, including 1,354 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 0.12 (1354 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ITGB1-DT NR_184020.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.583

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGB1-DT	NR_184020.1	n.961C>T		non_coding_transcript_exon_variant	3/3
IATPR	NR_160030.1	n.338-7049G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB1-DT	ENST00000450890.5	n.978C>T		non_coding_transcript_exon_variant	4/4	3
IATPR	ENST00000688819.2	n.320-7049G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17467 AN: 152058 Hom.: 1337 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0833

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0213

Gnomad FIN AF: 0.0873

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0852

Gnomad OTH AF: 0.102

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.115 AC: 17527 AN: 152176 Hom.: 1354 Cov.: 32 AF XY: 0.113 AC XY: 8410 AN XY: 74386

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.0832

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0213

Gnomad4 FIN AF: 0.0873

Gnomad4 NFE AF: 0.0852

Gnomad4 OTH AF: 0.101

Alfa AF: 0.105 Hom.: 113

Bravo AF: 0.119

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11009218; hg19: chr10-33370960;