Variant 13-23936911-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The variant allele was found at a frequency of 0.608 in 148,206 control chromosomes in the GnomAD database, including 28,065 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 0.61 ( 28065 hom., cov: 25)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.39

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.04).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.23936911C>T		intergenic_region
ANKRD20A19P	NR_073430.1 linkuse as main transcript	n.3861+4379G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.608

AC:

90054

AN:

148102

Hom.:

28064

Cov.:

show subpopulations

Gnomad AFR

AF:

0.490

Gnomad AMI

AF:

0.530

Gnomad AMR

AF:

0.489

Gnomad ASJ

AF:

0.547

Gnomad EAS

AF:

0.741

Gnomad SAS

AF:

0.654

Gnomad FIN

AF:

0.764

Gnomad MID

AF:

0.537

Gnomad NFE

AF:

0.672

Gnomad OTH

AF:

0.602

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.608

AC:

90088

AN:

148206

Hom.:

28065

Cov.:

AF XY:

0.607

AC XY:

43792

AN XY:

72100

show subpopulations

Gnomad4 AFR

AF:

0.490

Gnomad4 AMR

AF:

0.489

Gnomad4 ASJ

AF:

0.547

Gnomad4 EAS

AF:

0.740

Gnomad4 SAS

AF:

0.654

Gnomad4 FIN

AF:

0.764

Gnomad4 NFE

AF:

0.672

Gnomad4 OTH

AF:

0.599

Alfa

AF:

0.644

Hom.:

51237

Bravo

AF:

0.576

Asia WGS

AF:

0.666

AC:

2315

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.6

DANN

Benign

0.24

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