rs1990624

chr16-50643065-C-Achr16-50643065-C-T

Variant summary

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

The NM_033119.5(NKD1):c.*9284C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 152,140 control chromosomes in the GnomAD database, including 27,827 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 0.59 (27803 hom., cov: 32)
  • Exomes 𝑓: 0.74 (24 hom.)
• Consequence: NKD1 NM_033119.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237

Genes affected

NKD1 (HGNC:17045): (NKD inhibitor of WNT signaling pathway 1) In the mouse, Nkd is a Dishevelled (see DVL1; MIM 601365)-binding protein that functions as a negative regulator of the Wnt (see WNT1; MIM 164820)-beta-catenin (see MIM 116806)-Tcf (see MIM 602272) signaling pathway.[supplied by OMIM, Jun 2003]

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 = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NKD1	NM_033119.5	c.*9284C>A		3_prime_UTR_variant	10/10	ENST00000268459.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NKD1	ENST00000268459.6	c.*9284C>A		3_prime_UTR_variant	10/10	1	NM_033119.5	P1

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90425 AN: 151938 Hom.: 27800 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.584

GnomAD4 exome AF: 0.744 AC: 64 AN: 86 Hom.: 24 Cov.: 0 AF XY: 0.773 AC XY: 51 AN XY: 66

Gnomad4 AFR exome AF: 0.750

Gnomad4 AMR exome AF: 1.00

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.773

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.595 AC: 90455 AN: 152054 Hom.: 27803 Cov.: 32 AF XY: 0.596 AC XY: 44297 AN XY: 74324

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.583

Alfa AF: 0.556 Hom.: 1792

Bravo AF: 0.575

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.1
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1990624; hg19: chr16-50676976;