chr1-10430054-T-C

Position:

• chr1-10430054-T-C

Variant summary

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

The ENST00000607572.1(ENSG00000271989):​n.624A>G 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 0.545 in 157,476 control chromosomes in the GnomAD database, including 24,028 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 0.55 (23460 hom., cov: 32)
  • Exomes 𝑓: 0.43 (568 hom.)
• Consequence: ENSG00000271989 ENST00000607572.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21

Genes affected

ENSG00000271989 (HGNC:):

CENPS-CORT (HGNC:38843): (CENPS-CORT readthrough) This locus represents naturally occurring read-through transcription between the neighboring APITD1 (apoptosis-inducing, TAF9-like domain 1) and CORT (cortistatin) genes. Alternative splicing results in multiple transcript variants, two of which encode fusion proteins that share sequence identity with the products of each individual gene. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.10430054T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000271989	ENST00000607572.1	n.624A>G		non_coding_transcript_exon_variant	1/1	6
CENPS-CORT	ENST00000400900.6	c.-464T>C		upstream_gene_variant		2		ENSP00000383692.2

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83392 AN: 151930 Hom.: 23425 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.546

GnomAD4 exome AF: 0.427 AC: 2318 AN: 5428 Hom.: 568 Cov.: 0 AF XY: 0.438 AC XY: 1285 AN XY: 2934

Gnomad4 AFR exome AF: 0.566

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.430

Gnomad4 EAS exome AF: 0.419

Gnomad4 SAS exome AF: 0.520

Gnomad4 FIN exome AF: 0.355

Gnomad4 NFE exome AF: 0.394

Gnomad4 OTH exome AF: 0.419

GnomAD4 genome AF: 0.549 AC: 83481 AN: 152048 Hom.: 23460 Cov.: 32 AF XY: 0.552 AC XY: 41066 AN XY: 74336

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.551

Alfa AF: 0.485 Hom.: 8721

Bravo AF: 0.559

Asia WGS AF: 0.586 AC: 2039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.4
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs649101; hg19: chr1-10490111;