rs2765086

Variant names:

• chr13-23930816-C-T
• rs2765086
• ENST00000793729.1:n.741+10474G>A

Variant summary

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

The NR_073430.1(ANKRD20A19P):​n.3861+10474G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0638 in 151,424 control chromosomes in the GnomAD database, including 346 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 0.064 (346 hom., cov: 32)
• Consequence: ANKRD20A19P NR_073430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566
• Publications: 6 publications found

Genes affected

ENSG00000290660 (HGNC:):

ANKRD20A19P (HGNC:42737): (ankyrin repeat domain 20 family member A19, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0964 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_073430.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD20A19P	NR_073430.1		n.3861+10474G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290660	ENST00000793729.1		n.741+10474G>A		intron	N/A
	ENSG00000290660	ENST00000793730.1		n.338+10474G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0638 AC: 9654 AN: 151330 Hom.: 347 Cov.: 32

Gnomad AFR AF: 0.0991

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0395

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.0343

Gnomad SAS AF: 0.0237

Gnomad FIN AF: 0.0702

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0548

Gnomad OTH AF: 0.0608

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

GnomAD4 genome AF: 0.0638 AC: 9657 AN: 151424 Hom.: 346 Cov.: 32 AF XY: 0.0628 AC XY: 4643 AN XY: 73958

African (AFR) AF: 0.0989 AC: 4082 AN: 41274

American (AMR) AF: 0.0394 AC: 599 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.0248 AC: 86 AN: 3466

East Asian (EAS) AF: 0.0342 AC: 177 AN: 5168

South Asian (SAS) AF: 0.0240 AC: 115 AN: 4796

European-Finnish (FIN) AF: 0.0702 AC: 728 AN: 10372

Middle Eastern (MID) AF: 0.0445 AC: 13 AN: 292

European-Non Finnish (NFE) AF: 0.0548 AC: 3718 AN: 67852

Other (OTH) AF: 0.0606 AC: 127 AN: 2096

Alfa AF: 0.0526 Hom.: 227

Bravo AF: 0.0618

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.49
DANN	Benign	0.95
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs2765086; hg19: chr13-24504955;