3-64452368-G-C

Variant names:

• chr3-64452368-G-C
• rs9837159
• ENST00000762005.1:n.343G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000762005.1(PRICKLE2-DT):​n.343G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: PRICKLE2-DT ENST00000762005.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520
• Publications: 2 publications found

Genes affected

PRICKLE2-DT (HGNC:52829): (PRICKLE2 divergent transcript)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRICKLE2-DT	NR_183712.1	n.443+1737G>C		intron_variant	Intron 3 of 3
PRICKLE2-DT	NR_183714.1	n.345+1737G>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRICKLE2-DT	ENST00000762005.1	n.343G>C		non_coding_transcript_exon_variant	Exon 4 of 4
PRICKLE2-DT	ENST00000487097.1	n.469+1737G>C		intron_variant	Intron 3 of 3	4
PRICKLE2-DT	ENST00000659263.1	n.315+1737G>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.43
PhyloP100		-0.052

Splicing

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

Other links and lift over

dbSNP: rs9837159; hg19: chr3-64438044;