13-23932631-A-G

Position:

• chr13-23932631-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 0.38 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.23932631A>G		intergenic_region
ANKRD20A19P	NR_073430.1	n.3861+8659T>C		intron_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.415

Alfa AF: 0.373 Hom.: 14146

Bravo AF: 0.393

Asia WGS AF: 0.354 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2765089; hg19: chr13-24506770;