rs12876596

Positions:

• chr13-23947346-C-T

Variant summary

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

The NR_073430.1(ANKRD20A19P):​n.1970G>A 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 0.238 in 150,544 control chromosomes in the GnomAD database, including 5,266 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 (5266 hom., cov: 32)
• Consequence: ANKRD20A19P NR_073430.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

Genes affected

ANKRD20A19P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD20A19P	NR_073430.1	n.1970G>A		non_coding_transcript_exon_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.238 AC: 35811 AN: 150428 Hom.: 5268 Cov.: 32

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.221

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.252

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.238 AC: 35805 AN: 150544 Hom.: 5266 Cov.: 32 AF XY: 0.231 AC XY: 17007 AN XY: 73626

Gnomad4 AFR AF: 0.0608

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.249

Alfa AF: 0.307 Hom.: 9440

Bravo AF: 0.225

Asia WGS AF: 0.190 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.72
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: rs12876596; hg19: chr13-24521485; COSMIC: COSV69739128;