dbSNP rs554995: ANKRD20A5P:n.203+1116T>A (chr18-14180713-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000431648.8(ANKRD20A5P):n.203+1116T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000076 in 131,502 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000076 ( 0 hom., cov: 22)

Consequence

ANKRD20A5P
ENST00000431648.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.236

Publications

1 publications found

Variant links:

Genes affected

ANKRD20A5P (HGNC:33833): (ankyrin repeat domain 20 family member A5, pseudogene)

ANKRD20A5P links:

ANKRD20A5P (HGNC:):

ANKRD20A5P links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD20A5P	NR_040113.1 link	n.501+1116T>A		intron_variant	Intron 1 of 15

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ANKRD20A5P	ENST00000431648.8 link	n.203+1116T>A	intron_variant	Intron 1 of 21	6
ANKRD20A5P	ENST00000580995.2 link	n.316+1116T>A	intron_variant	Intron 2 of 13	5
ANKRD20A5P	ENST00000581181.6 link	n.643+1116T>A	intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.00000760

AC:

AN:

131502

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000155

Gnomad OTH

AF:

0.00

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

GnomAD4 genome

AF:

0.00000760

AC:

AN:

131502

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

61760

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

34944

American (AMR)

AF:

0.00

AC:

AN:

12372

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3368

East Asian (EAS)

AF:

0.00

AC:

AN:

4724

South Asian (SAS)

AF:

0.00

AC:

AN:

4416

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3992

Middle Eastern (MID)

AF:

0.00

AC:

AN:

266

European-Non Finnish (NFE)

AF:

0.0000155

AC:

AN:

64724

Other (OTH)

AF:

0.00

AC:

AN:

1810

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

1.3

(source)

DANN

Benign

0.095

PhyloP100

-0.24

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over