rs477274

Positions:

• chr13-75239418-C-A

Variant summary

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

The NR_027466.1(CTAGE11P):​n.964G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 1,613,304 control chromosomes in the GnomAD database, including 201,504 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 0.46 (16977 hom., cov: 32)
  • Exomes 𝑓: 0.50 (184527 hom.)
• Consequence: CTAGE11P NR_027466.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810

Genes affected

CTAGE11P (HGNC:37293): (CTAGE family member 11, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTAGE11P	NR_027466.1	n.964G>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTAGE11P	ENST00000451540.1	n.879G>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70518 AN: 151908 Hom.: 16959 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.468

GnomAD4 exome AF: 0.496 AC: 724988 AN: 1461278 Hom.: 184527 Cov.: 113 AF XY: 0.503 AC XY: 365941 AN XY: 726930

Gnomad4 AFR exome AF: 0.346

Gnomad4 AMR exome AF: 0.578

Gnomad4 ASJ exome AF: 0.442

Gnomad4 EAS exome AF: 0.655

Gnomad4 SAS exome AF: 0.737

Gnomad4 FIN exome AF: 0.513

Gnomad4 NFE exome AF: 0.473

Gnomad4 OTH exome AF: 0.501

GnomAD4 genome AF: 0.464 AC: 70562 AN: 152026 Hom.: 16977 Cov.: 32 AF XY: 0.474 AC XY: 35230 AN XY: 74306

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.472

Alfa AF: 0.469 Hom.: 4139

Bravo AF: 0.455

Asia WGS AF: 0.714 AC: 2482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.0
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs477274; hg19: chr13-75813554;