Variant chr6-31380588-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000424108.1(ZDHHC20P2):n.178G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0814 in 142,182 control chromosomes in the GnomAD database, including 592 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 0.081 ( 589 hom., cov: 33)

Exomes 𝑓: 0.15 ( 3 hom. )

Consequence

ZDHHC20P2
ENST00000424108.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0100

Variant links:

Genes affected

ZDHHC20P2 (HGNC:33457): (zinc finger DHHC-type containing 20 pseudogene 2)

ZDHHC20P2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZDHHC20P2	ENST00000424108.1 linkuse as main transcript	n.178G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.0814

AC:

11545

AN:

141914

Hom.:

589

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0390

Gnomad AMI

AF:

0.154

Gnomad AMR

AF:

0.0413

Gnomad ASJ

AF:

0.0482

Gnomad EAS

AF:

0.00545

Gnomad SAS

AF:

0.0707

Gnomad FIN

AF:

0.0875

Gnomad MID

AF:

0.0327

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.0626

GnomAD4 exome

AF:

0.147

AC:

AN:

150

Hom.:

Cov.:

AF XY:

0.122

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0333

Gnomad4 NFE exome

AF:

0.212

Gnomad4 OTH exome

AF:

0.100

GnomAD4 genome

AF:

0.0813

AC:

11549

AN:

142032

Hom.:

589

Cov.:

AF XY:

0.0774

AC XY:

5321

AN XY:

68736

show subpopulations

Gnomad4 AFR

AF:

0.0390

Gnomad4 AMR

AF:

0.0412

Gnomad4 ASJ

AF:

0.0482

Gnomad4 EAS

AF:

0.00525

Gnomad4 SAS

AF:

0.0720

Gnomad4 FIN

AF:

0.0875

Gnomad4 NFE

AF:

0.121

Gnomad4 OTH

AF:

0.0619

Alfa

AF:

0.110

Hom.:

423

Bravo

AF:

0.0700

Asia WGS

AF:

0.0210

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

8.8

DANN

Benign

0.49

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