chr14-69471805-T-C

Variant names:

• chr14-69471805-T-C
• rs1466255
• XM_017021290.1:c.-146+3339T>C

Variant summary

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

The XM_017021290.1(PLEKHD1):​c.-146+3339T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,908 control chromosomes in the GnomAD database, including 17,697 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 0.48 (17697 hom., cov: 31)
• Consequence: PLEKHD1 XM_017021290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339
• Publications: 7 publications found

Genes affected

PLEKHD1 (HGNC:20148): (pleckstrin homology and coiled-coil domain containing D1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72746 AN: 151790 Hom.: 17683 Cov.: 31

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.479 AC: 72800 AN: 151908 Hom.: 17697 Cov.: 31 AF XY: 0.482 AC XY: 35768 AN XY: 74210

African (AFR) AF: 0.456 AC: 18896 AN: 41404

American (AMR) AF: 0.402 AC: 6142 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2004 AN: 3470

East Asian (EAS) AF: 0.333 AC: 1720 AN: 5162

South Asian (SAS) AF: 0.564 AC: 2717 AN: 4818

European-Finnish (FIN) AF: 0.553 AC: 5822 AN: 10528

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33808 AN: 67942

Other (OTH) AF: 0.481 AC: 1017 AN: 2114

Alfa AF: 0.491 Hom.: 56826

Bravo AF: 0.461

Asia WGS AF: 0.442 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.1
DANN	Benign	0.61
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1466255; hg19: chr14-69938522;