13-23936911-C-T

Variant names:

• chr13-23936911-C-T
• rs2492084
• ENST00000793729.1:n.741+4379G>A

Variant summary

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

The ENST00000793729.1(ENSG00000290660):​n.741+4379G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 148,206 control chromosomes in the GnomAD database, including 28,065 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 0.61 (28065 hom., cov: 25)
• Consequence: ENSG00000290660 ENST00000793729.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 4 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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD20A19P	NR_073430.1	n.3861+4379G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290660	ENST00000793729.1	n.741+4379G>A		intron_variant	Intron 4 of 5
ENSG00000290660	ENST00000793730.1	n.338+4379G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.608 AC: 90054 AN: 148102 Hom.: 28064 Cov.: 25

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.537

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.608 AC: 90088 AN: 148206 Hom.: 28065 Cov.: 25 AF XY: 0.607 AC XY: 43792 AN XY: 72100

African (AFR) AF: 0.490 AC: 19428 AN: 39666

American (AMR) AF: 0.489 AC: 7186 AN: 14700

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1887 AN: 3448

East Asian (EAS) AF: 0.740 AC: 3701 AN: 5000

South Asian (SAS) AF: 0.654 AC: 3085 AN: 4718

European-Finnish (FIN) AF: 0.764 AC: 7534 AN: 9856

Middle Eastern (MID) AF: 0.529 AC: 145 AN: 274

European-Non Finnish (NFE) AF: 0.672 AC: 45409 AN: 67580

Other (OTH) AF: 0.599 AC: 1236 AN: 2064

Alfa AF: 0.631 Hom.: 81559

Bravo AF: 0.576

Asia WGS AF: 0.666 AC: 2315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.24
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2492084; hg19: chr13-24511050; COSMIC: COSV69739105;