rs1990624

Variant names:

• chr16-50643065-C-A
• rs1990624
• NM_033119.5:c.*9284C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-50643065-C-A
• chr16-50643065-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033119.5. 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
	NKD1	NM_033119.5	MANE Select	c.*9284C>A		3_prime_UTR	Exon 10 of 10	NP_149110.1	Q969G9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKD1	ENST00000268459.6	TSL:1 MANE Select	c.*9284C>A		3_prime_UTR	Exon 10 of 10	ENSP00000268459.3	Q969G9

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

African (AFR) AF: 0.750 AC: 3 AN: 4

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.773 AC: 51 AN: 66

Other (OTH) AF: 0.500 AC: 5 AN: 10

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

African (AFR) AF: 0.472 AC: 19580 AN: 41450

American (AMR) AF: 0.535 AC: 8170 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2357 AN: 3472

East Asian (EAS) AF: 0.532 AC: 2745 AN: 5156

South Asian (SAS) AF: 0.448 AC: 2158 AN: 4816

European-Finnish (FIN) AF: 0.748 AC: 7922 AN: 10596

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45399 AN: 67972

Other (OTH) AF: 0.583 AC: 1228 AN: 2108

Alfa AF: 0.550 Hom.: 1871

Bravo AF: 0.575

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.67
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs1990624; hg19: chr16-50676976;