rs13379889

Positions:

• chr15-90651808-A-G

Variant summary

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

The NR_120372.1(CRTC3-AS1):​n.294-10551T>C 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 0.262 in 151,894 control chromosomes in the GnomAD database, including 5,374 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 0.26 (5374 hom., cov: 31)
• Consequence: CRTC3-AS1 NR_120372.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

Genes affected

CRTC3-AS1 (HGNC:51433): (CRTC3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRTC3-AS1	NR_120372.1	n.294-10551T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRTC3-AS1	ENST00000559531.1	n.295-10551T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39801 AN: 151776 Hom.: 5368 Cov.: 31

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.262 AC: 39832 AN: 151894 Hom.: 5374 Cov.: 31 AF XY: 0.265 AC XY: 19695 AN XY: 74216

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.243

Alfa AF: 0.240 Hom.: 6297

Bravo AF: 0.268

Asia WGS AF: 0.286 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13379889; hg19: chr15-91195039;