rs1569783

Variant names:

• chr1-53781598-C-G
• rs1569783
• NM_018087.5:c.1800+5560G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-53781598-C-G
• chr1-53781598-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018087.5(NDC1):​c.1800+5560G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 152,190 control chromosomes in the GnomAD database, including 54,684 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 0.84 (54684 hom., cov: 32)
• Consequence: NDC1 NM_018087.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68
• Publications: 2 publications found

Genes affected

NDC1 (HGNC:25525): (NDC1 transmembrane nucleoporin) A structural constituent of nuclear pore. Involved in nuclear pore complex assembly and nuclear pore localization. Located in actin cytoskeleton; nuclear membrane; and plasma membrane. Part of nuclear pore. [provided by Alliance of Genome Resources, Apr 2022]

NDC1 Gene-Disease associations (from GenCC):

• polyneuropathy

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDC1	NM_018087.5	c.1800+5560G>C		intron_variant	Intron 16 of 17	ENST00000371429.4	NP_060557.3
NDC1	NM_001168551.2	c.1680+5560G>C		intron_variant	Intron 16 of 17		NP_001162023.1
NDC1	NR_033142.2	n.1714+5560G>C		intron_variant	Intron 15 of 16
NDC1	XM_011541766.3	c.1797+5560G>C		intron_variant	Intron 16 of 17		XP_011540068.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NDC1	ENST00000371429.4	c.1800+5560G>C		intron_variant	Intron 16 of 17	1	NM_018087.5	ENSP00000360483.3

Frequencies

GnomAD3 genomes AF: 0.844 AC: 128313 AN: 152072 Hom.: 54636 Cov.: 32

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.844 AC: 128408 AN: 152190 Hom.: 54684 Cov.: 32 AF XY: 0.841 AC XY: 62566 AN XY: 74406

African (AFR) AF: 0.912 AC: 37878 AN: 41524

American (AMR) AF: 0.666 AC: 10164 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.847 AC: 2940 AN: 3470

East Asian (EAS) AF: 0.747 AC: 3863 AN: 5170

South Asian (SAS) AF: 0.824 AC: 3972 AN: 4820

European-Finnish (FIN) AF: 0.863 AC: 9154 AN: 10604

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.846 AC: 57549 AN: 68016

Other (OTH) AF: 0.843 AC: 1783 AN: 2114

Alfa AF: 0.812 Hom.: 2624

Bravo AF: 0.830

Asia WGS AF: 0.798 AC: 2775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	20
DANN	Benign	0.85
PhyloP100		1.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs1569783; hg19: chr1-54247271;