Genetic Variant NM_205846.3:c.75+4699G>A (chr5-145830478-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.250

Publications

4 publications found

Variant links:

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]

PRELID2 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_205846.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

Gene	Transcript	Tags	HGVSc	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

Gene	Transcript	Tags	HGVSc	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.:

show subpopulations

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.:

AF XY:

0.709

AC XY:

52689

AN XY:

74298

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1474

2949

4423

5898

7372

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

826

1652

2478

3304

4130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.50

PhyloP100

-0.25

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over