rs7902627

Variant names:

• chr10-33116159-A-C
• rs7902627
• ENST00000414308.2:n.339+312T>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000414308.2(IATPR):​n.339+312T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,242 control chromosomes in the GnomAD database, including 3,456 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 0.19 (3456 hom., cov: 33)
• Consequence: IATPR ENST00000414308.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 7 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414308.2. 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.337+312T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IATPR	ENST00000414308.2	TSL:3	n.339+312T>G		intron	N/A
	IATPR	ENST00000688819.3		n.347+312T>G		intron	N/A
	ITGB1-DT	ENST00000821378.1		n.574-18409A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29227 AN: 152124 Hom.: 3444 Cov.: 33

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.192 AC: 29264 AN: 152242 Hom.: 3456 Cov.: 33 AF XY: 0.192 AC XY: 14273 AN XY: 74422

African (AFR) AF: 0.338 AC: 14023 AN: 41512

American (AMR) AF: 0.129 AC: 1972 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 496 AN: 3472

East Asian (EAS) AF: 0.234 AC: 1215 AN: 5184

South Asian (SAS) AF: 0.183 AC: 880 AN: 4814

European-Finnish (FIN) AF: 0.132 AC: 1405 AN: 10612

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8805 AN: 68022

Other (OTH) AF: 0.170 AC: 358 AN: 2112

Alfa AF: 0.192 Hom.: 2226

Bravo AF: 0.197

Asia WGS AF: 0.242 AC: 842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	17
DANN	Benign	0.79
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs7902627; hg19: chr10-33405087;