rs10493473

chr1-70382532-A-G

Variant summary

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

The ENST00000531950.1(ANKRD13C-DT):n.460-2726A>G 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 0.169 in 152,178 control chromosomes in the GnomAD database, including 2,316 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 0.17 (2316 hom., cov: 32)
• Consequence: ANKRD13C-DT ENST00000531950.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

Genes affected

ANKRD13C-DT (HGNC:4906): (ANKRD13C divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD13C-DT	ENST00000531950.1	n.460-2726A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25757 AN: 152060 Hom.: 2314 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.169 AC: 25768 AN: 152178 Hom.: 2316 Cov.: 32 AF XY: 0.167 AC XY: 12411 AN XY: 74396

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.177

Alfa AF: 0.179 Hom.: 402

Bravo AF: 0.167

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.4
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493473; hg19: chr1-70848215;