rs17286683

Positions:

• chr5-140401510-A-C
• chr5-140401510-A-G
• chr5-140401510-A-T

Variant summary

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

The 5-140401510-A-C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 158,782 control chromosomes in the GnomAD database, including 3,408 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 0.18 (3236 hom., cov: 32)
  • Exomes 𝑓: 0.21 (172 hom.)
• Consequence: ANKHD1-DT ENST00000666403.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

Genes affected

ANKHD1-DT (HGNC:55564): (ANKHD1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKHD1-DT	ENST00000666403.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27549 AN: 152140 Hom.: 3227 Cov.: 32

Gnomad AFR AF: 0.0441

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.185

GnomAD4 exome AF: 0.215 AC: 1401 AN: 6524 Hom.: 172 AF XY: 0.223 AC XY: 794 AN XY: 3568

Gnomad4 AFR exome AF: 0.0714

Gnomad4 AMR exome AF: 0.183

Gnomad4 ASJ exome AF: 0.219

Gnomad4 EAS exome AF: 0.292

Gnomad4 SAS exome AF: 0.239

Gnomad4 FIN exome AF: 0.285

Gnomad4 NFE exome AF: 0.216

Gnomad4 OTH exome AF: 0.178

GnomAD4 genome AF: 0.181 AC: 27565 AN: 152258 Hom.: 3236 Cov.: 32 AF XY: 0.184 AC XY: 13674 AN XY: 74446

Gnomad4 AFR AF: 0.0439

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.187

Alfa AF: 0.174 Hom.: 934

Bravo AF: 0.169

Asia WGS AF: 0.284 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	13
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17286683; hg19: chr5-139781095;