Genetic Variant ENSG00000289027:c.2025+32852G>C (chr7-92180343-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000692281.1(ENSG00000289027):c.2025+32852G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,060 control chromosomes in the GnomAD database, including 16,201 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 0.45 ( 16201 hom., cov: 32)

Exomes 𝑓: 0.28 ( 0 hom. )

Consequence

ENSG00000289027
ENST00000692281.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.432

Publications

10 publications found

Variant links:

Genes affected

ENSG00000289027 (HGNC:):

ENSG00000289027 links:

CYP51A1-AS1 (HGNC:50694): (CYP51A1 antisense RNA 1)

CYP51A1-AS1 links:

Genome browser will be placed here

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=-0.77).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP51A1-AS1	NR_122109.1 link	n.2616C>G		non_coding_transcript_exon_variant	Exon 5 of 5
CYP51A1-AS1	NR_122110.1 link	n.2098C>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289027	ENST00000692281.1 link	c.2025+32852G>C		intron_variant	Intron 17 of 25			ENSP00000510568.1
ENSG00000285953	ENST00000458493.6 link	c.2026-21140G>C		intron_variant	Intron 16 of 19	4		ENSP00000396352.2

Frequencies

GnomAD3 genomes

AF:

0.446

AC:

67788

AN:

151924

Hom.:

16173

Cov.:

show subpopulations

Gnomad AFR

AF:

0.617

Gnomad AMI

AF:

0.235

Gnomad AMR

AF:

0.378

Gnomad ASJ

AF:

0.543

Gnomad EAS

AF:

0.203

Gnomad SAS

AF:

0.364

Gnomad FIN

AF:

0.377

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.391

Gnomad OTH

AF:

0.452

GnomAD4 exome

AF:

0.278

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.200

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.446

AC:

67870

AN:

152042

Hom.:

16201

Cov.:

AF XY:

0.442

AC XY:

32814

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.617

AC:

25582

AN:

41468

American (AMR)

AF:

0.378

AC:

5768

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.543

AC:

1883

AN:

3470

East Asian (EAS)

AF:

0.203

AC:

1048

AN:

5172

South Asian (SAS)

AF:

0.365

AC:

1760

AN:

4816

European-Finnish (FIN)

AF:

0.377

AC:

3983

AN:

10578

Middle Eastern (MID)

AF:

0.405

AC:

119

AN:

294

European-Non Finnish (NFE)

AF:

0.391

AC:

26563

AN:

67968

Other (OTH)

AF:

0.452

AC:

950

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1845

3690

5536

7381

9226

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

604

1208

1812

2416

3020

<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:

0.417

Hom.:

1713

Bravo

AF:

0.453

Asia WGS

AF:

0.336

AC:

1172

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

(source)

DANN

Benign

0.80

PhyloP100

0.43

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over