chr13-23932631-A-G

Variant names:

• chr13-23932631-A-G
• rs2765089
• ENST00000793729.1:n.741+8659T>C

Variant summary

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

The ENST00000793729.1(ENSG00000290660):​n.741+8659T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 150,986 control chromosomes in the GnomAD database, including 11,163 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 0.38 (11163 hom., cov: 33)
• Consequence: ENSG00000290660 ENST00000793729.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 5 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793729.1. 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
	ANKRD20A19P	NR_073430.1		n.3861+8659T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290660	ENST00000793729.1		n.741+8659T>C		intron	N/A
	ENSG00000290660	ENST00000793730.1		n.338+8659T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57248 AN: 150868 Hom.: 11149 Cov.: 33

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.380 AC: 57303 AN: 150986 Hom.: 11163 Cov.: 33 AF XY: 0.383 AC XY: 28175 AN XY: 73636

African (AFR) AF: 0.378 AC: 15674 AN: 41418

American (AMR) AF: 0.522 AC: 7886 AN: 15108

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1500 AN: 3466

East Asian (EAS) AF: 0.298 AC: 1500 AN: 5040

South Asian (SAS) AF: 0.366 AC: 1711 AN: 4670

European-Finnish (FIN) AF: 0.315 AC: 3246 AN: 10318

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24352 AN: 67680

Other (OTH) AF: 0.415 AC: 864 AN: 2084

Alfa AF: 0.372 Hom.: 18362

Bravo AF: 0.393

Asia WGS AF: 0.354 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.9
DANN	Benign	0.73
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2765089; hg19: chr13-24506770;