rs1993593

chr8-109277352-C-T

Variant summary

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

The NM_032869.4(NUDCD1):c.1029-1856G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0977 in 152,100 control chromosomes in the GnomAD database, including 774 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 0.098 (774 hom., cov: 32)
• Consequence: NUDCD1 NM_032869.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.29

Genes affected

NUDCD1 (HGNC:24306): (NudC domain containing 1) Predicted to be involved in immune system process. Located in cytosol and nucleoplasm. [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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NUDCD1	NM_032869.4	c.1029-1856G>A		intron_variant		ENST00000239690.9
NUDCD1	NM_001128211.2	c.942-1856G>A		intron_variant
NUDCD1	XM_047422330.1	c.768-1856G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUDCD1	ENST00000239690.9	c.1029-1856G>A		intron_variant		1	NM_032869.4	P1

Frequencies

GnomAD3 genomes AF: 0.0978 AC: 14862 AN: 151984 Hom.: 773 Cov.: 32

Gnomad AFR AF: 0.0882

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0529

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0503

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.0977 AC: 14866 AN: 152100 Hom.: 774 Cov.: 32 AF XY: 0.0949 AC XY: 7059 AN XY: 74358

Gnomad4 AFR AF: 0.0882

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.0527

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0503

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.124

Alfa AF: 0.108 Hom.: 483

Bravo AF: 0.102

Asia WGS AF: 0.0770 AC: 273 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.031
Dann	Benign	0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1993593; hg19: chr8-110289581;