Variant rs28615950 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_040090.1(CYP21A1P):n.1064G>A 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 0.0947 in 1,506,258 control chromosomes in the GnomAD database, including 19,973 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 0.10 ( 1866 hom., cov: 29)

Exomes 𝑓: 0.094 ( 18107 hom. )

Consequence

CYP21A1P
NR_040090.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.696

Variant links:

Genes affected

(HGNC:):

links:

CYP21A1P (HGNC:2599): (cytochrome P450 family 21 subfamily A member 1, pseudogene)

CYP21A1P links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP21A1P	NR_040090.1 linkuse as main transcript	n.1064G>A		non_coding_transcript_exon_variant	3/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000342991.10 linkuse as main transcript	n.1064G>A		non_coding_transcript_exon_variant	3/8	3
CYP21A1P	ENST00000354927.4 linkuse as main transcript	n.626G>A		non_coding_transcript_exon_variant	5/10

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

15117

AN:

144392

Hom.:

1871

Cov.:

show subpopulations

Gnomad AFR

AF:

0.141

Gnomad AMI

AF:

0.215

Gnomad AMR

AF:

0.0778

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.0372

Gnomad SAS

AF:

0.169

Gnomad FIN

AF:

0.0603

Gnomad MID

AF:

0.105

Gnomad NFE

AF:

0.0915

Gnomad OTH

AF:

0.121

GnomAD3 exomes

AF:

0.0995

AC:

16313

AN:

163982

Hom.:

1976

AF XY:

0.103

AC XY:

8984

AN XY:

87026

show subpopulations

Gnomad AFR exome

AF:

0.153

Gnomad AMR exome

AF:

0.0737

Gnomad ASJ exome

AF:

0.173

Gnomad EAS exome

AF:

0.0362

Gnomad SAS exome

AF:

0.151

Gnomad FIN exome

AF:

0.0608

Gnomad NFE exome

AF:

0.0961

Gnomad OTH exome

AF:

0.108

GnomAD4 exome

AF:

0.0936

AC:

127503

AN:

1361756

Hom.:

18107

Cov.:

AF XY:

0.0950

AC XY:

63905

AN XY:

672492

show subpopulations

Gnomad4 AFR exome

AF:

0.156

Gnomad4 AMR exome

AF:

0.0763

Gnomad4 ASJ exome

AF:

0.171

Gnomad4 EAS exome

AF:

0.0204

Gnomad4 SAS exome

AF:

0.151

Gnomad4 FIN exome

AF:

0.0603

Gnomad4 NFE exome

AF:

0.0897

Gnomad4 OTH exome

AF:

0.104

GnomAD4 genome

AF:

0.105

AC:

15117

AN:

144502

Hom.:

1866

Cov.:

AF XY:

0.104

AC XY:

7323

AN XY:

70466

show subpopulations

Gnomad4 AFR

AF:

0.141

Gnomad4 AMR

AF:

0.0777

Gnomad4 ASJ

AF:

0.165

Gnomad4 EAS

AF:

0.0375

Gnomad4 SAS

AF:

0.168

Gnomad4 FIN

AF:

0.0603

Gnomad4 NFE

AF:

0.0915

Gnomad4 OTH

AF:

0.119

Alfa

AF:

0.0705

Hom.:

169

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.3

DANN

Benign

0.80

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over