Variant rs2297246 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_027270.1(ANKRD20A11P):n.281A>C 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 0.514 in 1,023,356 control chromosomes in the GnomAD database, including 110,573 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 0.66 ( 33827 hom., cov: 33)

Exomes 𝑓: 0.49 ( 76746 hom. )

Consequence

ANKRD20A11P
NR_027270.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.869

Variant links:

Genes affected

ANKRD20A11P (HGNC:42024): (ankyrin repeat domain 20 family member A11, pseudogene)

ANKRD20A11P 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD20A11P	NR_027270.1 linkuse as main transcript	n.281A>C		non_coding_transcript_exon_variant	1/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD20A11P	ENST00000344693.5 linkuse as main transcript	n.274A>C		non_coding_transcript_exon_variant	1/6	1

Frequencies

GnomAD3 genomes

AF:

0.657

AC:

99827

AN:

151960

Hom.:

33752

Cov.:

show subpopulations

Gnomad AFR

AF:

0.811

Gnomad AMI

AF:

0.615

Gnomad AMR

AF:

0.675

Gnomad ASJ

AF:

0.637

Gnomad EAS

AF:

0.788

Gnomad SAS

AF:

0.705

Gnomad FIN

AF:

0.542

Gnomad MID

AF:

0.599

Gnomad NFE

AF:

0.566

Gnomad OTH

AF:

0.631

GnomAD4 exome

AF:

0.489

AC:

425655

AN:

871282

Hom.:

76746

Cov.:

AF XY:

0.492

AC XY:

202503

AN XY:

411332

show subpopulations

Gnomad4 AFR exome

AF:

0.688

Gnomad4 AMR exome

AF:

0.667

Gnomad4 ASJ exome

AF:

0.561

Gnomad4 EAS exome

AF:

0.686

Gnomad4 SAS exome

AF:

0.629

Gnomad4 FIN exome

AF:

0.515

Gnomad4 NFE exome

AF:

0.473

Gnomad4 OTH exome

AF:

0.519

GnomAD4 genome

AF:

0.657

AC:

99961

AN:

152074

Hom.:

33827

Cov.:

AF XY:

0.658

AC XY:

48924

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.812

Gnomad4 AMR

AF:

0.675

Gnomad4 ASJ

AF:

0.637

Gnomad4 EAS

AF:

0.789

Gnomad4 SAS

AF:

0.705

Gnomad4 FIN

AF:

0.542

Gnomad4 NFE

AF:

0.566

Gnomad4 OTH

AF:

0.635

Alfa

AF:

0.448

Hom.:

1062

Bravo

AF:

0.675

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.5

DANN

Benign

0.31

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