Variant rs41315836 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000342991.10(ENSG00000290788):n.1274T>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 0.218 in 1,341,104 control chromosomes in the GnomAD database, including 90,030 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 0.32 ( 11437 hom., cov: 26)

Exomes 𝑓: 0.21 ( 78593 hom. )

Consequence

ENSG00000290788
ENST00000342991.10 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.03

Variant links:

Genes affected

ENSG00000290788 (HGNC:):

ENSG00000290788 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=-0.68).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP21A1P	NR_040090.1 linkuse as main transcript	n.1274T>G		non_coding_transcript_exon_variant	5/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290788	ENST00000342991.10 linkuse as main transcript	n.1274T>G		non_coding_transcript_exon_variant	5/8	3
CYP21A1P	ENST00000354927.4 linkuse as main transcript	n.836T>G		non_coding_transcript_exon_variant	7/10	6

Frequencies

GnomAD3 genomes

AF:

0.324

AC:

44500

AN:

137376

Hom.:

11424

Cov.:

show subpopulations

Gnomad AFR

AF:

0.546

Gnomad AMI

AF:

0.246

Gnomad AMR

AF:

0.284

Gnomad ASJ

AF:

0.265

Gnomad EAS

AF:

0.204

Gnomad SAS

AF:

0.420

Gnomad FIN

AF:

0.134

Gnomad MID

AF:

0.340

Gnomad NFE

AF:

0.240

Gnomad OTH

AF:

0.359

GnomAD3 exomes

AF:

0.253

AC:

56949

AN:

225024

Hom.:

15165

AF XY:

0.261

AC XY:

32075

AN XY:

122742

show subpopulations

Gnomad AFR exome

AF:

0.565

Gnomad AMR exome

AF:

0.180

Gnomad ASJ exome

AF:

0.201

Gnomad EAS exome

AF:

0.195

Gnomad SAS exome

AF:

0.431

Gnomad FIN exome

AF:

0.133

Gnomad NFE exome

AF:

0.223

Gnomad OTH exome

AF:

0.253

GnomAD4 exome

AF:

0.206

AC:

248476

AN:

1203630

Hom.:

78593

Cov.:

AF XY:

0.213

AC XY:

127899

AN XY:

601202

show subpopulations

Gnomad4 AFR exome

AF:

0.572

Gnomad4 AMR exome

AF:

0.173

Gnomad4 ASJ exome

AF:

0.208

Gnomad4 EAS exome

AF:

0.214

Gnomad4 SAS exome

AF:

0.421

Gnomad4 FIN exome

AF:

0.134

Gnomad4 NFE exome

AF:

0.181

Gnomad4 OTH exome

AF:

0.242

GnomAD4 genome

AF:

0.324

AC:

44544

AN:

137474

Hom.:

11437

Cov.:

AF XY:

0.320

AC XY:

21427

AN XY:

67016

show subpopulations

Gnomad4 AFR

AF:

0.546

Gnomad4 AMR

AF:

0.284

Gnomad4 ASJ

AF:

0.265

Gnomad4 EAS

AF:

0.204

Gnomad4 SAS

AF:

0.418

Gnomad4 FIN

AF:

0.134

Gnomad4 NFE

AF:

0.240

Gnomad4 OTH

AF:

0.355

Alfa

AF:

0.283

Hom.:

1748

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

DANN

Benign

0.90

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

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