rs1569783

chr1-53781598-C-Gchr1-53781598-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
NDC1	NM_018087.5	c.1800+5560G>C		intron_variant		ENST00000371429.4
NDC1	NM_001168551.2	c.1680+5560G>C		intron_variant
NDC1	XM_011541766.3	c.1797+5560G>C		intron_variant
NDC1	NR_033142.2	n.1714+5560G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NDC1	ENST00000371429.4	c.1800+5560G>C		intron_variant		1	NM_018087.5	P1

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

Gnomad4 AFR AF: 0.912

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.847

Gnomad4 EAS AF: 0.747

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.863

Gnomad4 NFE AF: 0.846

Gnomad4 OTH AF: 0.843

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1569783; hg19: chr1-54247271;