18-14180713-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_040113.1(ANKRD20A5P):n.501+1116T>C variant causes a intron, non coding transcript 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 NR_040113.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ANKRD20A5P	NR_040113.1	n.501+1116T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD20A5P	ENST00000431648.8	n.203+1116T>C		intron_variant, non_coding_transcript_variant
	ENST00000581363.5	n.228+1116T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000581181.5	n.455+1116T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000581935.5	n.501+1116T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.867

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.703

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs554995; hg19: chr18-14180712;