rs10493473

Variant names:

• chr1-70382532-A-G
• rs10493473
• ENST00000531950.1:n.460-2726A>G

Variant summary

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

The ENST00000531950.1(ANKRD13C-DT):​n.460-2726A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000531950.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD13C-DT	ENST00000531950.1	TSL:5	n.460-2726A>G		intron	N/A

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

African (AFR) AF: 0.145 AC: 6021 AN: 41526

American (AMR) AF: 0.135 AC: 2065 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3468

East Asian (EAS) AF: 0.109 AC: 563 AN: 5172

South Asian (SAS) AF: 0.160 AC: 772 AN: 4828

European-Finnish (FIN) AF: 0.155 AC: 1637 AN: 10588

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13430 AN: 68000

Other (OTH) AF: 0.177 AC: 374 AN: 2112

Alfa AF: 0.178 Hom.: 411

Bravo AF: 0.167

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.61
PhyloP100		-0.45
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10493473;

hg19: chr1-70848215;