rs11009218

Variant names:

• chr10-33082032-C-T
• rs11009218
• ENST00000414157.3:n.970C>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.970C>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 ENST00000414157.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.583
• 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=-0.88).
• 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 rank	MANE	Protein	UniProt
ITGB1-DT	NR_184020.1	n.961C>T		non_coding_transcript_exon_variant	Exon 3 of 3
IATPR	NR_160030.1	n.338-7049G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB1-DT	ENST00000414157.3	n.970C>T		non_coding_transcript_exon_variant	Exon 3 of 3	1
ITGB1-DT	ENST00000450890.6	n.1311C>T		non_coding_transcript_exon_variant	Exon 4 of 4	3
ITGB1-DT	ENST00000666298.2	n.1474C>T		non_coding_transcript_exon_variant	Exon 4 of 4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.212 AC: 8809 AN: 41484

American (AMR) AF: 0.0832 AC: 1272 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 350 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.0213 AC: 103 AN: 4826

European-Finnish (FIN) AF: 0.0873 AC: 924 AN: 10584

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0852 AC: 5796 AN: 68020

Other (OTH) AF: 0.101 AC: 212 AN: 2108

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
PhyloP100		0.58
Mutation Taster		=99/1	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11009218; hg19: chr10-33370960;