rs13379889

Variant names:

• chr15-90651808-A-G
• rs13379889
• ENST00000559531.2:n.333-10551T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000559531.2(CRTC3-AS1):​n.333-10551T>C variant causes a intron 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 ENST00000559531.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CRTC3-AS1	NR_120372.1	n.294-10551T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRTC3-AS1	ENST00000559531.2	n.333-10551T>C		intron_variant	Intron 2 of 3	3
CRTC3-AS1	ENST00000764740.1	n.294-10551T>C		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.282 AC: 11676 AN: 41426

American (AMR) AF: 0.311 AC: 4748 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 781 AN: 3464

East Asian (EAS) AF: 0.327 AC: 1692 AN: 5168

South Asian (SAS) AF: 0.235 AC: 1132 AN: 4818

European-Finnish (FIN) AF: 0.278 AC: 2916 AN: 10502

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16157 AN: 67958

Other (OTH) AF: 0.243 AC: 513 AN: 2110

Alfa AF: 0.242 Hom.: 9696

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
PhyloP100		-0.0080

Splicing

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

Other links and lift over

dbSNP: rs13379889; hg19: chr15-91195039;