chr13-23922979-A-G

Variant names:

• chr13-23922979-A-G
• rs6490847
• ENST00000793729.1:n.742-13738T>C

Variant summary

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

The ENST00000793729.1(ENSG00000290660):​n.742-13738T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,060 control chromosomes in the GnomAD database, including 4,040 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 0.20 (4040 hom., cov: 32)
• Consequence: ENSG00000290660 ENST00000793729.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.368 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.3862-13738T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290660	ENST00000793729.1		n.742-13738T>C		intron	N/A
	ENSG00000290660	ENST00000793730.1		n.339-13734T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31033 AN: 151942 Hom.: 4021 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.0584

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.205 AC: 31100 AN: 152060 Hom.: 4040 Cov.: 32 AF XY: 0.202 AC XY: 15028 AN XY: 74312

African (AFR) AF: 0.373 AC: 15442 AN: 41436

American (AMR) AF: 0.135 AC: 2056 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 531 AN: 3472

East Asian (EAS) AF: 0.0305 AC: 158 AN: 5180

South Asian (SAS) AF: 0.0589 AC: 284 AN: 4822

European-Finnish (FIN) AF: 0.161 AC: 1696 AN: 10556

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10292 AN: 67994

Other (OTH) AF: 0.186 AC: 393 AN: 2114

Alfa AF: 0.172 Hom.: 7388

Bravo AF: 0.213

Asia WGS AF: 0.0610 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.9
DANN	Benign	0.79
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs6490847; hg19: chr13-24497118;