rs7902627

Positions:

• chr10-33116159-A-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_160030.1(IATPR):​n.337+312T>G 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 0.192 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 NR_160030.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IATPR	NR_160030.1	n.337+312T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IATPR	ENST00000688819.2	n.319+312T>G		intron_variant, non_coding_transcript_variant
IATPR	ENST00000414308.1	n.202+312T>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.170

Alfa AF: 0.160 Hom.: 573

Bravo AF: 0.197

Asia WGS AF: 0.242 AC: 842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7902627; hg19: chr10-33405087;