Genetic Variant ENSG00000271989:n.624A>G (chr1-10430054-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.21

Publications

8 publications found

Variant links:

Genes affected

ENSG00000271989 (HGNC:):

ENSG00000271989 links:

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]

CENPS-CORT links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607572.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000271989	ENST00000607572.1	TSL:6	n.624A>G		non_coding_transcript_exon	Exon 1 of 1
	CENPS-CORT	ENST00000400900.6	TSL:2	c.-464T>C		upstream_gene	N/A	ENSP00000383692.2

Frequencies

GnomAD3 genomes

AF:

0.549

AC:

83392

AN:

151930

Hom.:

23425

Cov.:

show subpopulations

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.:

AF XY:

0.438

AC XY:

1285

AN XY:

2934

show subpopulations

African (AFR)

AF:

0.566

AC:

AN:

106

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.430

AC:

AN:

172

East Asian (EAS)

AF:

0.419

AC:

AN:

South Asian (SAS)

AF:

0.520

AC:

597

AN:

1148

European-Finnish (FIN)

AF:

0.355

AC:

AN:

220

Middle Eastern (MID)

AF:

0.409

AC:

AN:

European-Non Finnish (NFE)

AF:

0.394

AC:

1293

AN:

3278

Other (OTH)

AF:

0.419

AC:

144

AN:

344

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

108

163

217

271

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.549

AC:

83481

AN:

152048

Hom.:

23460

Cov.:

AF XY:

0.552

AC XY:

41066

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.673

AC:

27906

AN:

41492

American (AMR)

AF:

0.569

AC:

8687

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.482

AC:

1672

AN:

3470

East Asian (EAS)

AF:

0.470

AC:

2429

AN:

5172

South Asian (SAS)

AF:

0.579

AC:

2789

AN:

4814

European-Finnish (FIN)

AF:

0.518

AC:

5468

AN:

10554

Middle Eastern (MID)

AF:

0.568

AC:

167

AN:

294

European-Non Finnish (NFE)

AF:

0.481

AC:

32692

AN:

67960

Other (OTH)

AF:

0.551

AC:

1161

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1930

3860

5789

7719

9649

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

710

1420

2130

2840

3550

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.487

Hom.:

9853

Bravo

AF:

0.559

Asia WGS

AF:

0.586

AC:

2039

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.4

(source)

DANN

Benign

0.80

PhyloP100

-2.2

PromoterAI

0.057

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over