rs12876596

Variant names:

• chr13-23947346-C-T
• rs12876596
• NR_073430.1:n.1970G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_073430.1(ANKRD20A19P):​n.1970G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 150,544 control chromosomes in the GnomAD database, including 5,266 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 0.24 (5266 hom., cov: 32)
• Consequence: ANKRD20A19P NR_073430.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 2 publications found

Genes affected

ANKRD20A19P (HGNC:42737): (ankyrin repeat domain 20 family member A19, pseudogene)

ENSG00000290660 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD20A19P	NR_073430.1	n.1970G>A		non_coding_transcript_exon_variant	Exon 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290660	ENST00000793729.1	n.205-1355G>A		intron_variant	Intron 1 of 5
ENSG00000290660	ENST00000793731.1	n.222-1366G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.238 AC: 35811 AN: 150428 Hom.: 5268 Cov.: 32

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.221

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.238 AC: 35805 AN: 150544 Hom.: 5266 Cov.: 32 AF XY: 0.231 AC XY: 17007 AN XY: 73626

African (AFR) AF: 0.0608 AC: 2434 AN: 40060

American (AMR) AF: 0.233 AC: 3559 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3468

East Asian (EAS) AF: 0.261 AC: 1342 AN: 5136

South Asian (SAS) AF: 0.209 AC: 1007 AN: 4820

European-Finnish (FIN) AF: 0.280 AC: 2963 AN: 10592

Middle Eastern (MID) AF: 0.228 AC: 66 AN: 290

European-Non Finnish (NFE) AF: 0.334 AC: 22693 AN: 67928

Other (OTH) AF: 0.249 AC: 519 AN: 2088

Alfa AF: 0.296 Hom.: 12514

Bravo AF: 0.225

Asia WGS AF: 0.190 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.72
DANN	Benign	0.30
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs12876596; hg19: chr13-24521485; COSMIC: COSV69739128;