rs2297246

Positions:

• chr21-13980164-T-G
• chr21-13980164-T-C

Variant summary

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

The NR_027270.1(ANKRD20A11P):​n.281A>C 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 0.514 in 1,023,356 control chromosomes in the GnomAD database, including 110,573 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 (33827 hom., cov: 33)
  • Exomes 𝑓: 0.49 (76746 hom.)
• Consequence: ANKRD20A11P NR_027270.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.869

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD20A11P	NR_027270.1	n.281A>C		non_coding_transcript_exon_variant	1/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD20A11P	ENST00000344693.5	n.274A>C		non_coding_transcript_exon_variant	1/6	1

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99827 AN: 151960 Hom.: 33752 Cov.: 33

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.631

GnomAD4 exome AF: 0.489 AC: 425655 AN: 871282 Hom.: 76746 Cov.: 20 AF XY: 0.492 AC XY: 202503 AN XY: 411332

Gnomad4 AFR exome AF: 0.688

Gnomad4 AMR exome AF: 0.667

Gnomad4 ASJ exome AF: 0.561

Gnomad4 EAS exome AF: 0.686

Gnomad4 SAS exome AF: 0.629

Gnomad4 FIN exome AF: 0.515

Gnomad4 NFE exome AF: 0.473

Gnomad4 OTH exome AF: 0.519

GnomAD4 genome AF: 0.657 AC: 99961 AN: 152074 Hom.: 33827 Cov.: 33 AF XY: 0.658 AC XY: 48924 AN XY: 74336

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.705

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.635

Alfa AF: 0.448 Hom.: 1062

Bravo AF: 0.675

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.5
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2297246; hg19: chr21-15352485; COSMIC: COSV60951785;