rs477274

Variant names:

• chr13-75239418-C-A
• rs477274
• ENST00000451540.1:n.879G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_027466.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTAGE11P	NR_027466.1		n.964G>T		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTAGE11P	ENST00000451540.1	TSL:6	n.879G>T		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.346 AC: 11583 AN: 33476

American (AMR) AF: 0.578 AC: 25814 AN: 44690

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 11560 AN: 26130

East Asian (EAS) AF: 0.655 AC: 25988 AN: 39686

South Asian (SAS) AF: 0.737 AC: 63515 AN: 86232

European-Finnish (FIN) AF: 0.513 AC: 27379 AN: 53404

Middle Eastern (MID) AF: 0.568 AC: 3134 AN: 5516

European-Non Finnish (NFE) AF: 0.473 AC: 525753 AN: 1111782

Other (OTH) AF: 0.501 AC: 30262 AN: 60362

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

African (AFR) AF: 0.349 AC: 14474 AN: 41468

American (AMR) AF: 0.514 AC: 7844 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1514 AN: 3464

East Asian (EAS) AF: 0.684 AC: 3528 AN: 5158

South Asian (SAS) AF: 0.758 AC: 3657 AN: 4824

European-Finnish (FIN) AF: 0.520 AC: 5480 AN: 10548

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32541 AN: 67970

Other (OTH) AF: 0.472 AC: 999 AN: 2116

Alfa AF: 0.468 Hom.: 4631

Bravo AF: 0.455

Asia WGS AF: 0.714 AC: 2482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.0
DANN	Benign	0.75
PhyloP100		0.081

Splicing

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

Other links and lift over

dbSNP: rs477274; hg19: chr13-75813554;