rs11950106

Variant names:

• chr5-145543674-G-T
• rs11950106
• XM_047416828.1:c.*11-27835C>A

Variant summary

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

The ENST00000510259.5(PRELID2):​n.71-70359C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 151,972 control chromosomes in the GnomAD database, including 3,473 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 0.19 (3473 hom., cov: 32)
• Consequence: PRELID2 ENST00000510259.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 2 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=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510259.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRELID2	ENST00000510259.5	TSL:3	n.71-70359C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28078 AN: 151854 Hom.: 3459 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0677

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.185 AC: 28136 AN: 151972 Hom.: 3473 Cov.: 32 AF XY: 0.180 AC XY: 13346 AN XY: 74286

African (AFR) AF: 0.358 AC: 14813 AN: 41380

American (AMR) AF: 0.143 AC: 2186 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 668 AN: 3468

East Asian (EAS) AF: 0.0675 AC: 349 AN: 5174

South Asian (SAS) AF: 0.109 AC: 524 AN: 4810

European-Finnish (FIN) AF: 0.100 AC: 1064 AN: 10608

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8094 AN: 67974

Other (OTH) AF: 0.170 AC: 359 AN: 2108

Alfa AF: 0.135 Hom.: 1032

Bravo AF: 0.197

Asia WGS AF: 0.108 AC: 377 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	13
DANN	Benign	0.68
PhyloP100		1.0

Splicing

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.

Other links and lift over

dbSNP: rs11950106;

hg19: chr5-144923237;