18-14180713-T-C

Variant names:

• chr18-14180713-T-C
• rs554995
• ENST00000431648.8:n.203+1116T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000431648.8(ANKRD20A5P):​n.203+1116T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 131,298 control chromosomes in the GnomAD database, including 32,974 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 (32974 hom., cov: 22)
• Consequence: ANKRD20A5P ENST00000431648.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236
• Publications: 1 publications found

Genes affected

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

ANKRD20A5P (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD20A5P	ENST00000431648.8	n.203+1116T>C		intron_variant	Intron 1 of 21	6
ANKRD20A5P	ENST00000580995.2	n.316+1116T>C		intron_variant	Intron 2 of 13	5
ANKRD20A5P	ENST00000581181.6	n.643+1116T>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.662 AC: 86917 AN: 131290 Hom.: 32976 Cov.: 22

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.662 AC: 86903 AN: 131298 Hom.: 32974 Cov.: 22 AF XY: 0.658 AC XY: 40574 AN XY: 61658

African (AFR) AF: 0.277 AC: 9668 AN: 34920

American (AMR) AF: 0.738 AC: 9121 AN: 12358

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2800 AN: 3366

East Asian (EAS) AF: 0.371 AC: 1742 AN: 4694

South Asian (SAS) AF: 0.802 AC: 3515 AN: 4382

European-Finnish (FIN) AF: 0.867 AC: 3454 AN: 3984

Middle Eastern (MID) AF: 0.789 AC: 191 AN: 242

European-Non Finnish (NFE) AF: 0.841 AC: 54347 AN: 64644

Other (OTH) AF: 0.703 AC: 1280 AN: 1822

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.18
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs554995; hg19: chr18-14180712;