Variant chr2-169767711-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000448589.1(KLHL23):c.44-8730C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 222,526 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 32)

Exomes 𝑓: 0.000018 ( 0 hom. )

Consequence

KLHL23
ENST00000448589.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.305

Variant links:

Genes affected

KLHL23 (HGNC:27506): (kelch like family member 23)

KLHL23 links:

PTCHD3P2 (HGNC:):

PTCHD3P2 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTCHD3P2	use as main transcript	n.169767711C>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Protein	UniProt
KLHL23	ENST00000437875.1 linkuse as main transcript	c.830-5609C>G	intron_variant	3	ENSP00000394732.1	H7C0F4
KLHL23	ENST00000448589.1 linkuse as main transcript	c.44-8730C>G	intron_variant	2	ENSP00000400833.1	H7C1K9
PTCHD3P2	ENST00000424937.1 linkuse as main transcript	n.1087+2G>C	splice_donor_variant, intron_variant	6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.0000180

AC:

AN:

222526

Hom.:

Cov.:

AF XY:

0.00000789

AC XY:

AN XY:

126682

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000480

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000250

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Benign

0.83

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over