rs151361

Positions:

• chr20-59038947-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRELID3B	NM_016045.3	c.33-313T>C		intron_variant		ENST00000355937.9
SLMO2-ATP5E	NR_037930.1	n.149-2187T>C		intron_variant, non_coding_transcript_variant
PRELID3B	NM_001256403.2	c.33-313T>C		intron_variant
SLMO2-ATP5E	NR_037929.1	n.149-313T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRELID3B	ENST00000355937.9	c.33-313T>C		intron_variant		1	NM_016045.3	P1
PRELID3B	ENST00000371033.9	c.33-313T>C		intron_variant		2
PRELID3B	ENST00000463057.1	c.33-313T>C		intron_variant, NMD_transcript_variant		3
PRELID3B	ENST00000466051.1	n.112-313T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.227

Alfa AF: 0.226 Hom.: 5632

Bravo AF: 0.226

Asia WGS AF: 0.147 AC: 511 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.4
DANN	Benign	0.74

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: rs151361; hg19: chr20-57614002;