rs384843

Variant names:

• chr1-16593976-G-A
• rs384843
• ENST00000430580.6:c.-317-409C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000430580.6(NBPF1):​c.-317-409C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: NBPF1 ENST00000430580.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393
• Publications: 3 publications found

Genes affected

NBPF1 (HGNC:26088): (NBPF member 1) This gene is a member of the neuroblastoma breakpoint family (NBPF) which consists of dozens of recently duplicated genes primarily located in segmental duplications on human chromosome 1. This gene family has experienced its greatest expansion within the human lineage and has expanded, to a lesser extent, among primates in general. Members of this gene family are characterized by tandemly repeated copies of DUF1220 protein domains. Gene copy number variations in the human chromosomal region 1q21.1, where most DUF1220 domains are located, have been implicated in a number of developmental and neurogenetic diseases such as microcephaly, macrocephaly, autism, schizophrenia, cognitive disability, congenital heart disease, neuroblastoma, and congenital kidney and urinary tract anomalies. Altered expression of some gene family members is associated with several types of cancer. This gene family contains numerous pseudogenes. [provided by RefSeq, Apr 2013]

ENSG00000271732 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NBPF1	NM_001405667.2	c.-503-223C>T		intron_variant	Intron 4 of 28		NP_001392596.1
NBPF1	NM_001405680.2	c.-317-409C>T		intron_variant	Intron 4 of 28		NP_001392609.1
NBPF1	NM_001405681.2	c.-503-223C>T		intron_variant	Intron 4 of 28		NP_001392610.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NBPF1	ENST00000430580.6	c.-317-409C>T		intron_variant	Intron 4 of 28	5		ENSP00000474456.1
NBPF1	ENST00000392963.5	n.-190-1663C>T		intron_variant	Intron 2 of 18	5		ENSP00000473795.1
NBPF1	ENST00000420513.1	n.297-223C>T		intron_variant	Intron 3 of 3	3
ENSG00000271732	ENST00000607700.2	n.137+2149G>A		intron_variant	Intron 2 of 2	6

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 145740 Hom.: 0 Cov.: 22

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 145740 Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 70856

African (AFR) AF: 0.00 AC: 0 AN: 38090

American (AMR) AF: 0.00 AC: 0 AN: 14746

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3444

East Asian (EAS) AF: 0.00 AC: 0 AN: 5022

South Asian (SAS) AF: 0.00 AC: 0 AN: 4562

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9522

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 308

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67134

Other (OTH) AF: 0.00 AC: 0 AN: 2008

Alfa AF: 0.400 Hom.: 16

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.5
DANN	Benign	0.34
PhyloP100		-0.39
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs384843; hg19: chr1-16920471; COSMIC: COSV67429061;