rs1458925

Positions:

• chr8-109257964-T-C

Variant summary

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

The NM_032869.4(NUDCD1):​c.1300-12483A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,866 control chromosomes in the GnomAD database, including 20,430 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 0.51 (20430 hom., cov: 32)
• Consequence: NUDCD1 NM_032869.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NUDCD1	NM_032869.4	c.1300-12483A>G		intron_variant		ENST00000239690.9
NUDCD1	NM_001128211.2	c.1213-12483A>G		intron_variant
NUDCD1	XM_047422330.1	c.1039-12483A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUDCD1	ENST00000239690.9	c.1300-12483A>G		intron_variant		1	NM_032869.4	P1

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77076 AN: 151748 Hom.: 20389 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.508 AC: 77173 AN: 151866 Hom.: 20430 Cov.: 32 AF XY: 0.511 AC XY: 37948 AN XY: 74214

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.481

Alfa AF: 0.479 Hom.: 2251

Bravo AF: 0.515

Asia WGS AF: 0.573 AC: 1990 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.64

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: rs1458925; hg19: chr8-110270193;