rs2054255

Positions:

• chr8-109261631-G-A

Variant summary

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

The NM_032869.4(NUDCD1):​c.1299+9374C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 149,210 control chromosomes in the GnomAD database, including 17,908 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 0.48 (17908 hom., cov: 31)
• Consequence: NUDCD1 NM_032869.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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 = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NUDCD1	NM_032869.4	c.1299+9374C>T		intron_variant		ENST00000239690.9
NUDCD1	NM_001128211.2	c.1212+9374C>T		intron_variant
NUDCD1	XM_047422330.1	c.1038+9374C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUDCD1	ENST00000239690.9	c.1299+9374C>T		intron_variant		1	NM_032869.4	P1

Frequencies

GnomAD3 genomes AF: 0.483 AC: 72022 AN: 149096 Hom.: 17872 Cov.: 31

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.483 AC: 72116 AN: 149210 Hom.: 17908 Cov.: 31 AF XY: 0.487 AC XY: 35528 AN XY: 72922

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.440

Alfa AF: 0.448 Hom.: 2579

Bravo AF: 0.480

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.17
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs2054255; hg19: chr8-110273860;