13-23908914-A-G

Variant names:

• chr13-23908914-A-G
• rs7337921
• ENST00000793729.1:n.885+184T>C

Variant summary

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

The ENST00000793729.1(ENSG00000290660):​n.885+184T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 151,978 control chromosomes in the GnomAD database, including 30,542 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 0.63 (30542 hom., cov: 32)
• Consequence: ENSG00000290660 ENST00000793729.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD20A19P	NR_073430.1	n.4005+184T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290660	ENST00000793729.1	n.885+184T>C		intron_variant	Intron 5 of 5
ENSG00000290660	ENST00000793730.1	n.486+184T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.632 AC: 95915 AN: 151860 Hom.: 30524 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.632 AC: 95982 AN: 151978 Hom.: 30542 Cov.: 32 AF XY: 0.628 AC XY: 46639 AN XY: 74306

African (AFR) AF: 0.630 AC: 26124 AN: 41434

American (AMR) AF: 0.734 AC: 11206 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2400 AN: 3472

East Asian (EAS) AF: 0.716 AC: 3696 AN: 5164

South Asian (SAS) AF: 0.685 AC: 3295 AN: 4808

European-Finnish (FIN) AF: 0.496 AC: 5232 AN: 10538

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41917 AN: 67980

Other (OTH) AF: 0.661 AC: 1394 AN: 2110

Alfa AF: 0.624 Hom.: 79274

Bravo AF: 0.649

Asia WGS AF: 0.705 AC: 2449 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.57
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs7337921; hg19: chr13-24483053; COSMIC: COSV69344438;