rs11072110

chr15-69695543-C-T

Variant summary

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

The NR_126437.1(PCAT29):n.611-124C>T 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 0.637 in 152,120 control chromosomes in the GnomAD database, including 31,063 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 0.64 (31056 hom., cov: 32)
  • Exomes 𝑓: 0.50 (7 hom.)
• Consequence: PCAT29 NR_126437.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68

Genes affected

DRAIC (HGNC:27082): (downregulated RNA in cancer, inhibitor of cell invasion and migration)

PCAT29 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCAT29	NR_126437.1	n.611-124C>T		intron_variant, non_coding_transcript_variant
PCAT29	NR_126438.1	n.378-124C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DRAIC	ENST00000646247.2	n.2152-124C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96731 AN: 151950 Hom.: 31014 Cov.: 32

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.649

GnomAD4 exome AF: 0.500 AC: 26 AN: 52 Hom.: 7 AF XY: 0.393 AC XY: 11 AN XY: 28

Gnomad4 FIN exome AF: 0.563

Gnomad4 NFE exome AF: 0.389

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.637 AC: 96816 AN: 152068 Hom.: 31056 Cov.: 32 AF XY: 0.637 AC XY: 47335 AN XY: 74344

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.646

Alfa AF: 0.625 Hom.: 9061

Bravo AF: 0.651

Asia WGS AF: 0.639 AC: 2221 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.068
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11072110; hg19: chr15-69987882;