rs6490847

Positions:

• chr13-23922979-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.23922979A>G		intergenic_region
ANKRD20A19P	NR_073430.1	n.3862-13738T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.0305

Gnomad4 SAS AF: 0.0589

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.186

Alfa AF: 0.160 Hom.: 2584

Bravo AF: 0.213

Asia WGS AF: 0.0610 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6490847; hg19: chr13-24497118;