rs6893183

Variant names:

• chr5-145638921-C-T
• rs6893183
• XM_047416828.1:c.*11-123082G>A

Variant summary

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

The ENST00000510259.5(PRELID2):​n.70+126010G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,184 control chromosomes in the GnomAD database, including 7,178 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 0.22 (7178 hom., cov: 32)
• Consequence: PRELID2 ENST00000510259.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRELID2	ENST00000510259.5	TSL:3	n.70+126010G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33876 AN: 152066 Hom.: 7140 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.0994

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0910

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0633

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.223 AC: 33972 AN: 152184 Hom.: 7178 Cov.: 32 AF XY: 0.222 AC XY: 16506 AN XY: 74402

African (AFR) AF: 0.552 AC: 22904 AN: 41484

American (AMR) AF: 0.247 AC: 3767 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0994 AC: 345 AN: 3470

East Asian (EAS) AF: 0.144 AC: 746 AN: 5176

South Asian (SAS) AF: 0.110 AC: 530 AN: 4826

European-Finnish (FIN) AF: 0.0910 AC: 965 AN: 10606

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0633 AC: 4308 AN: 68024

Other (OTH) AF: 0.175 AC: 370 AN: 2114

Alfa AF: 0.128 Hom.: 601

Bravo AF: 0.252

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.063
DANN	Benign	0.66
PhyloP100		-1.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6893183; hg19: chr5-145018484;