21-13980164-T-G

Variant names:

• chr21-13980164-T-G
• rs2297246
• ENST00000344693.6:n.274A>C

Variant summary

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

The ENST00000344693.6(ENSG00000291280):​n.274A>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: ENSG00000291280 ENST00000344693.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.869
• Publications: 5 publications found

Genes affected

ENSG00000291280 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000344693.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD20A11P	NR_027270.1		n.281A>C		non_coding_transcript_exon	Exon 1 of 6

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291280	ENST00000344693.6	TSL:1	n.274A>C		non_coding_transcript_exon	Exon 1 of 8
	ENSG00000291280	ENST00000766858.1		n.473A>C		non_coding_transcript_exon	Exon 1 of 8
	ENSG00000291280	ENST00000766860.1		n.258A>C		non_coding_transcript_exon	Exon 1 of 11

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

African (AFR) AF: 0.688 AC: 10490 AN: 15256

American (AMR) AF: 0.667 AC: 3562 AN: 5340

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 4078 AN: 7266

East Asian (EAS) AF: 0.686 AC: 4566 AN: 6656

South Asian (SAS) AF: 0.629 AC: 20980 AN: 33346

European-Finnish (FIN) AF: 0.515 AC: 4902 AN: 9510

Middle Eastern (MID) AF: 0.503 AC: 950 AN: 1890

European-Non Finnish (NFE) AF: 0.473 AC: 360341 AN: 761586

Other (OTH) AF: 0.519 AC: 15786 AN: 30432

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

African (AFR) AF: 0.812 AC: 33698 AN: 41514

American (AMR) AF: 0.675 AC: 10318 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2210 AN: 3468

East Asian (EAS) AF: 0.789 AC: 4057 AN: 5140

South Asian (SAS) AF: 0.705 AC: 3404 AN: 4826

European-Finnish (FIN) AF: 0.542 AC: 5746 AN: 10594

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.566 AC: 38452 AN: 67928

Other (OTH) AF: 0.635 AC: 1341 AN: 2112

Alfa AF: 0.448 Hom.: 1062

Bravo AF: 0.675

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.5
DANN	Benign	0.31
PhyloP100		-0.87

Splicing

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

Other links and lift over

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