rs56270809

Positions:

• chr21-13979932-A-C

Variant summary

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

The NR_027270.1(ANKRD20A11P):​n.513T>G 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 0.266 in 1,245,642 control chromosomes in the GnomAD database, including 46,301 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 0.24 (4759 hom., cov: 30)
  • Exomes 𝑓: 0.27 (41542 hom.)
• Consequence: ANKRD20A11P NR_027270.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD20A11P	NR_027270.1	n.513T>G		non_coding_transcript_exon_variant	1/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD20A11P	ENST00000344693.5	n.506T>G		non_coding_transcript_exon_variant	1/6	1
ANKRD20A11P	ENST00000451663.5			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36648 AN: 151720 Hom.: 4743 Cov.: 30

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.0921

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.257

GnomAD4 exome AF: 0.269 AC: 294367 AN: 1093802 Hom.: 41542 Cov.: 15 AF XY: 0.272 AC XY: 151179 AN XY: 555816

Gnomad4 AFR exome AF: 0.163

Gnomad4 AMR exome AF: 0.344

Gnomad4 ASJ exome AF: 0.316

Gnomad4 EAS exome AF: 0.0876

Gnomad4 SAS exome AF: 0.339

Gnomad4 FIN exome AF: 0.218

Gnomad4 NFE exome AF: 0.273

Gnomad4 OTH exome AF: 0.264

GnomAD4 genome AF: 0.242 AC: 36707 AN: 151840 Hom.: 4759 Cov.: 30 AF XY: 0.240 AC XY: 17850 AN XY: 74230

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.0923

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.264

Alfa AF: 0.255 Hom.: 961

Bravo AF: 0.242

Asia WGS AF: 0.225 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56270809; hg19: chr21-15352253; COSMIC: COSV60948517;