20-59038947-A-G

Variant names:

• chr20-59038947-A-G
• rs151361
• NM_016045.3:c.33-313T>C

Variant summary

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

The NM_016045.3(PRELID3B):​c.33-313T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,168 control chromosomes in the GnomAD database, including 4,363 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 0.24 (4363 hom., cov: 33)
• Consequence: PRELID3B NM_016045.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410
• Publications: 28 publications found

Genes affected

PRELID3B (HGNC:15892): (PRELI domain containing 3B) 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]

SLMO2-ATP5E (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016045.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRELID3B	NM_016045.3	MANE Select	c.33-313T>C		intron	N/A	NP_057129.2
	PRELID3B	NM_001256403.2		c.33-313T>C		intron	N/A	NP_001243332.1
	SLMO2-ATP5E	NR_037929.1		n.149-313T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRELID3B	ENST00000355937.9	TSL:1 MANE Select	c.33-313T>C		intron	N/A	ENSP00000348206.4
	PRELID3B	ENST00000371033.9	TSL:2	c.33-313T>C		intron	N/A	ENSP00000360072.5
	PRELID3B	ENST00000463057.1	TSL:3	n.33-313T>C		intron	N/A	ENSP00000431440.1

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35817 AN: 152050 Hom.: 4358 Cov.: 33

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.236 AC: 35850 AN: 152168 Hom.: 4363 Cov.: 33 AF XY: 0.240 AC XY: 17847 AN XY: 74402

African (AFR) AF: 0.264 AC: 10955 AN: 41516

American (AMR) AF: 0.197 AC: 3005 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 868 AN: 3472

East Asian (EAS) AF: 0.121 AC: 628 AN: 5186

South Asian (SAS) AF: 0.172 AC: 829 AN: 4830

European-Finnish (FIN) AF: 0.342 AC: 3615 AN: 10564

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15308 AN: 67990

Other (OTH) AF: 0.227 AC: 479 AN: 2112

Alfa AF: 0.228 Hom.: 14007

Bravo AF: 0.226

Asia WGS AF: 0.147 AC: 511 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.4
DANN	Benign	0.74
PhyloP100		-0.41
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: rs151361; hg19: chr20-57614002;