rs1458926

Variant names:

• chr8-109258466-C-G
• rs1458926
• NM_032869.4:c.1299+12539G>C

Variant summary

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

The NM_032869.4(NUDCD1):​c.1299+12539G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,654 control chromosomes in the GnomAD database, including 10,676 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 0.36 (10676 hom., cov: 31)
• Consequence: NUDCD1 NM_032869.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 3 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUDCD1	NM_032869.4	c.1299+12539G>C		intron_variant	Intron 8 of 9	ENST00000239690.9	NP_116258.2
NUDCD1	NM_001128211.2	c.1212+12539G>C		intron_variant	Intron 8 of 9		NP_001121683.1
NUDCD1	XM_047422330.1	c.1038+12539G>C		intron_variant	Intron 8 of 9		XP_047278286.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUDCD1	ENST00000239690.9	c.1299+12539G>C		intron_variant	Intron 8 of 9	1	NM_032869.4	ENSP00000239690.4

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54638 AN: 151536 Hom.: 10670 Cov.: 31

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.360 AC: 54657 AN: 151654 Hom.: 10676 Cov.: 31 AF XY: 0.366 AC XY: 27110 AN XY: 74056

African (AFR) AF: 0.216 AC: 8918 AN: 41376

American (AMR) AF: 0.450 AC: 6835 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 874 AN: 3464

East Asian (EAS) AF: 0.472 AC: 2434 AN: 5158

South Asian (SAS) AF: 0.497 AC: 2386 AN: 4800

European-Finnish (FIN) AF: 0.452 AC: 4741 AN: 10498

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.400 AC: 27158 AN: 67866

Other (OTH) AF: 0.342 AC: 720 AN: 2104

Alfa AF: 0.382 Hom.: 1461

Bravo AF: 0.351

Asia WGS AF: 0.502 AC: 1746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.73
PhyloP100		-0.057
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: rs1458926; hg19: chr8-110270695; COSMIC: COSV53454631;