rs2765086

chr13-23930816-C-T

Variant summary

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

The NR_073430.1(ANKRD20A19P):n.3861+10474G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0638 in 151,424 control chromosomes in the GnomAD database, including 346 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 0.064 (346 hom., cov: 32)
• Consequence: ANKRD20A19P NR_073430.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566

Genes affected

ANKRD20A19P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD20A19P	NR_073430.1	n.3861+10474G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0638 AC: 9654 AN: 151330 Hom.: 347 Cov.: 32

Gnomad AFR AF: 0.0991

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0395

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.0343

Gnomad SAS AF: 0.0237

Gnomad FIN AF: 0.0702

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0548

Gnomad OTH AF: 0.0608

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

GnomAD4 genome AF: 0.0638 AC: 9657 AN: 151424 Hom.: 346 Cov.: 32 AF XY: 0.0628 AC XY: 4643 AN XY: 73958

Gnomad4 AFR AF: 0.0989

Gnomad4 AMR AF: 0.0394

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.0342

Gnomad4 SAS AF: 0.0240

Gnomad4 FIN AF: 0.0702

Gnomad4 NFE AF: 0.0548

Gnomad4 OTH AF: 0.0606

Alfa AF: 0.0527 Hom.: 204

Bravo AF: 0.0618

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	0.49
Dann	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2765086; hg19: chr13-24504955;