rs9510968

chr13-23938264-A-Gchr13-23938264-A-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+3026T>C 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 0.54 in 151,932 control chromosomes in the GnomAD database, including 23,297 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 0.54 (23297 hom., cov: 32)
• Consequence: ANKRD20A19P NR_073430.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

Genes affected

ANKRD20A19P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD20A19P	NR_073430.1	n.3861+3026T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82039 AN: 151814 Hom.: 23298 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.540 AC: 82068 AN: 151932 Hom.: 23297 Cov.: 32 AF XY: 0.541 AC XY: 40144 AN XY: 74258

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.535

Alfa AF: 0.595 Hom.: 43215

Bravo AF: 0.516

Asia WGS AF: 0.620 AC: 2155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.9
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9510968; hg19: chr13-24512403; COSMIC: COSV69739116;