17-47624914-T-C

Position:

• chr17-47624914-T-C

Variant summary

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

The ENST00000584391.6(KPNB1-DT):​n.225+1633A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,886 control chromosomes in the GnomAD database, including 16,719 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 0.46 (16719 hom., cov: 31)
• Consequence: KPNB1-DT ENST00000584391.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441

Genes affected

KPNB1-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KPNB1-DT	NR_171699.1	n.205-848A>G		intron_variant
KPNB1-DT	NR_171700.1	n.204+1633A>G		intron_variant
KPNB1-DT	NR_171701.1	n.357+1633A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KPNB1-DT	ENST00000582066.1	n.39+11598A>G		intron_variant		3
KPNB1-DT	ENST00000582389.5	n.178+1633A>G		intron_variant		5
KPNB1-DT	ENST00000584391.6	n.225+1633A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69341 AN: 151768 Hom.: 16717 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.457 AC: 69371 AN: 151886 Hom.: 16719 Cov.: 31 AF XY: 0.463 AC XY: 34368 AN XY: 74224

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.482

Alfa AF: 0.499 Hom.: 9764

Bravo AF: 0.449

Asia WGS AF: 0.594 AC: 2066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11079784; hg19: chr17-45702280;