5-145830478-C-T

Variant names:

• chr5-145830478-C-T
• rs443033
• NM_205846.3:c.75+4699G>A

Variant summary

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

The NM_205846.3(PRELID2):​c.75+4699G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 152,048 control chromosomes in the GnomAD database, including 39,965 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 0.71 (39965 hom., cov: 32)
• Consequence: PRELID2 NM_205846.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 4 publications found

Genes affected

PRELID2 (HGNC:28306): (PRELI domain containing 2) Predicted to enable phosphatidic acid transfer activity. Predicted to be involved in phospholipid transport. Predicted to be active in mitochondrial intermembrane space. [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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_205846.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRELID2	NM_205846.3	MANE Select	c.75+4699G>A		intron	N/A	NP_995318.1	Q8N945-3
	PRELID2	NM_182960.4		c.75+4699G>A		intron	N/A	NP_892005.1	Q8N945-1
	PRELID2	NM_138492.6		c.-215-4278G>A		intron	N/A	NP_612501.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRELID2	ENST00000683046.1	MANE Select	c.75+4699G>A		intron	N/A	ENSP00000506938.1	Q8N945-3
	PRELID2	ENST00000394450.6	TSL:1	c.-215-4278G>A		intron	N/A	ENSP00000377965.2	Q8N945-2
	PRELID2	ENST00000334744.8	TSL:2	c.75+4699G>A		intron	N/A	ENSP00000335675.4	Q8N945-1

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108531 AN: 151928 Hom.: 39957 Cov.: 32

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.714 AC: 108598 AN: 152048 Hom.: 39965 Cov.: 32 AF XY: 0.709 AC XY: 52689 AN XY: 74298

African (AFR) AF: 0.538 AC: 22296 AN: 41448

American (AMR) AF: 0.730 AC: 11154 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2678 AN: 3470

East Asian (EAS) AF: 0.527 AC: 2713 AN: 5150

South Asian (SAS) AF: 0.750 AC: 3610 AN: 4816

European-Finnish (FIN) AF: 0.745 AC: 7867 AN: 10564

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.820 AC: 55769 AN: 68000

Other (OTH) AF: 0.744 AC: 1574 AN: 2116

Alfa AF: 0.784 Hom.: 178387

Bravo AF: 0.702

Asia WGS AF: 0.633 AC: 2204 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.50
PhyloP100		-0.25
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: rs443033; hg19: chr5-145210041;