rs11079784

Variant names:

• chr17-47624914-T-A
• rs11079784
• ENST00000582066.2:n.262+11598A>T

Your query was ambiguous. Multiple possible variants found:

• chr17-47624914-T-A
• chr17-47624914-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000582066.2(KPNB1-DT):​n.262+11598A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: KPNB1-DT ENST00000582066.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441
• Publications: 35 publications found

Genes affected

KPNB1-DT (HGNC:55336): (KPNB1 divergent transcript)

NPEPPS (HGNC:7900): (aminopeptidase puromycin sensitive) This gene encodes the puromycin-sensitive aminopeptidase, a zinc metallopeptidase which hydrolyzes amino acids from the N-terminus of its substrate. The protein has been localized to both the cytoplasm and to cellular membranes. This enzyme degrades enkaphalins in the brain, and studies in mouse suggest that it is involved in proteolytic events regulating the cell cycle. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KPNB1-DT	NR_171699.1	n.205-848A>T		intron_variant	Intron 3 of 3
KPNB1-DT	NR_171700.1	n.204+1633A>T		intron_variant	Intron 3 of 3
KPNB1-DT	NR_171701.1	n.357+1633A>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KPNB1-DT	ENST00000582066.2	n.262+11598A>T		intron_variant	Intron 2 of 2	3
KPNB1-DT	ENST00000582389.6	n.313+1633A>T		intron_variant	Intron 3 of 3	5
KPNB1-DT	ENST00000584391.7	n.408+1633A>T		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.5
DANN	Benign	0.71
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs11079784; hg19: chr17-45702280;