rs2147990

Positions:

• chr13-23925110-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.3862-15869G>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 0.526 in 151,994 control chromosomes in the GnomAD database, including 23,361 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 0.53 (23361 hom., cov: 32)
• Consequence: ANKRD20A19P NR_073430.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

Genes affected

ANKRD20A19P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD20A19P	NR_073430.1	n.3862-15869G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80020 AN: 151876 Hom.: 23375 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.526 AC: 80005 AN: 151994 Hom.: 23361 Cov.: 32 AF XY: 0.526 AC XY: 39059 AN XY: 74300

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.537

Alfa AF: 0.619 Hom.: 60842

Bravo AF: 0.489

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.5
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2147990; hg19: chr13-24499249; COSMIC: COSV69344450;