Variant rs17147682 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001031710.3(KLHL7):c.121-5814A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00862 in 1,614,014 control chromosomes in the GnomAD database, including 598 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.022 ( 140 hom., cov: 32)

Exomes 𝑓: 0.0072 ( 458 hom. )

Consequence

KLHL7
NM_001031710.3 intron

Scores

Splicing: ADA: 0.0003823

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.43

Variant links:

Genes affected

KLHL7 (HGNC:15646): (kelch like family member 7) This gene encodes a BTB-Kelch-related protein. The encoded protein may be involved in protein degradation. Mutations in this gene have been associated with retinitis pigmentosa 42. [provided by RefSeq, Feb 2010]

KLHL7 links:

KLHL7 (HGNC:):

KLHL7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0012262166).

BP6

Variant 7-23117963-A-G is Benign according to our data. Variant chr7-23117963-A-G is described in ClinVar as [Benign]. Clinvar id is 802301.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KLHL7	NM_001031710.3 linkuse as main transcript	c.121-5814A>G		intron_variant		ENST00000339077.10	NP_001026880.2	Q8IXQ5-1A8K364

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KLHL7	ENST00000339077.10 linkuse as main transcript	c.121-5814A>G		intron_variant		1	NM_001031710.3	ENSP00000343273.4		Q8IXQ5-1

Frequencies

GnomAD3 genomes

AF:

0.0217

AC:

3295

AN:

152192

Hom.:

138

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0503

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0111

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.154

Gnomad SAS

AF:

0.0211

Gnomad FIN

AF:

0.00198

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.000794

Gnomad OTH

AF:

0.0220

GnomAD3 exomes

AF:

0.0195

AC:

4895

AN:

251292

Hom.:

268

AF XY:

0.0179

AC XY:

2436

AN XY:

135836

show subpopulations

Gnomad AFR exome

AF:

0.0506

Gnomad AMR exome

AF:

0.00651

Gnomad ASJ exome

AF:

0.00218

Gnomad EAS exome

AF:

0.164

Gnomad SAS exome

AF:

0.0170

Gnomad FIN exome

AF:

0.00265

Gnomad NFE exome

AF:

0.00161

Gnomad OTH exome

AF:

0.00848

GnomAD4 exome

AF:

0.00725

AC:

10596

AN:

1461704

Hom.:

458

Cov.:

AF XY:

0.00727

AC XY:

5288

AN XY:

727158

show subpopulations

Gnomad4 AFR exome

AF:

0.0511

Gnomad4 AMR exome

AF:

0.00631

Gnomad4 ASJ exome

AF:

0.00168

Gnomad4 EAS exome

AF:

0.130

Gnomad4 SAS exome

AF:

0.0169

Gnomad4 FIN exome

AF:

0.00340

Gnomad4 NFE exome

AF:

0.000705

Gnomad4 OTH exome

AF:

0.0152

GnomAD4 genome

AF:

0.0217

AC:

3311

AN:

152310

Hom.:

140

Cov.:

AF XY:

0.0220

AC XY:

1639

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.0505

Gnomad4 AMR

AF:

0.0111

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.155

Gnomad4 SAS

AF:

0.0217

Gnomad4 FIN

AF:

0.00198

Gnomad4 NFE

AF:

0.000779

Gnomad4 OTH

AF:

0.0213

Alfa

AF:

0.00870

Hom.:

Bravo

AF:

0.0238

TwinsUK

AF:

0.000539

AC:

ALSPAC

AF:

0.00104

AC:

ESP6500AA

AF:

0.0454

AC:

200

ESP6500EA

AF:

0.000581

AC:

ExAC

AF:

0.0198

AC:

2408

Asia WGS

AF:

0.0690

AC:

239

AN:

3478

EpiCase

AF:

0.00115

EpiControl

AF:

0.00154

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

PERCHING syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Mendelics

May 28, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.59

BayesDel_noAF

Benign

-0.48

CADD

Benign

DANN

Benign

0.81

Eigen

Benign

-0.27

Eigen_PC

Benign

-0.18

FATHMM_MKL

Benign

0.69

LIST_S2

Benign

0.29

MetaRNN

Benign

0.0012

MetaSVM

Benign

-1.1

PROVEAN

Benign

1.3

REVEL

Benign

0.069

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.13

Vest4

0.085

ClinPred

0.0018

GERP RS

3.4

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00038

dbscSNV1_RF

Benign

0.046

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over