21-13979932-A-C

Variant names:

• chr21-13979932-A-C
• rs56270809
• ENST00000344693.6:n.506T>G

Variant summary

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

The ENST00000344693.6(ENSG00000291280):​n.506T>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: ENSG00000291280 ENST00000344693.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 8 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=-0.9).
• 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 rank	MANE	Protein	UniProt
ANKRD20A11P	NR_027270.1	n.513T>G		non_coding_transcript_exon_variant	Exon 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291280	ENST00000344693.6	n.506T>G		non_coding_transcript_exon_variant	Exon 1 of 8	1
ENSG00000291280	ENST00000428576.6	n.217T>G		non_coding_transcript_exon_variant	Exon 1 of 9	3
ENSG00000291280	ENST00000766858.1	n.705T>G		non_coding_transcript_exon_variant	Exon 1 of 8

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

African (AFR) AF: 0.163 AC: 4302 AN: 26456

American (AMR) AF: 0.344 AC: 13045 AN: 37884

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 7013 AN: 22212

East Asian (EAS) AF: 0.0876 AC: 3253 AN: 37126

South Asian (SAS) AF: 0.339 AC: 25370 AN: 74898

European-Finnish (FIN) AF: 0.218 AC: 10629 AN: 48690

Middle Eastern (MID) AF: 0.293 AC: 988 AN: 3376

European-Non Finnish (NFE) AF: 0.273 AC: 217165 AN: 795352

Other (OTH) AF: 0.264 AC: 12602 AN: 47808

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

African (AFR) AF: 0.166 AC: 6892 AN: 41406

American (AMR) AF: 0.324 AC: 4955 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3464

East Asian (EAS) AF: 0.0923 AC: 474 AN: 5136

South Asian (SAS) AF: 0.337 AC: 1622 AN: 4808

European-Finnish (FIN) AF: 0.212 AC: 2238 AN: 10552

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18534 AN: 67890

Other (OTH) AF: 0.264 AC: 556 AN: 2104

Alfa AF: 0.261 Hom.: 1747

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
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

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