chr7-23114256-C-T

Variant summary

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

The NM_001031710.3(KLHL7):​c.120+8110C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 150,380 control chromosomes in the GnomAD database, including 18,346 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 0.46 ( 18346 hom., cov: 32)

Consequence

KLHL7
NM_001031710.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.361
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KLHL7NM_001031710.3 linkuse as main transcriptc.120+8110C>T intron_variant ENST00000339077.10 NP_001026880.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KLHL7ENST00000339077.10 linkuse as main transcriptc.120+8110C>T intron_variant 1 NM_001031710.3 ENSP00000343273 P1Q8IXQ5-1

Frequencies

GnomAD3 genomes
AF:
0.464
AC:
69653
AN:
150270
Hom.:
18306
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.759
Gnomad AMI
AF:
0.300
Gnomad AMR
AF:
0.353
Gnomad ASJ
AF:
0.388
Gnomad EAS
AF:
0.326
Gnomad SAS
AF:
0.266
Gnomad FIN
AF:
0.275
Gnomad MID
AF:
0.433
Gnomad NFE
AF:
0.375
Gnomad OTH
AF:
0.464
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.464
AC:
69736
AN:
150380
Hom.:
18346
Cov.:
32
AF XY:
0.453
AC XY:
33356
AN XY:
73578
show subpopulations
Gnomad4 AFR
AF:
0.759
Gnomad4 AMR
AF:
0.352
Gnomad4 ASJ
AF:
0.388
Gnomad4 EAS
AF:
0.326
Gnomad4 SAS
AF:
0.266
Gnomad4 FIN
AF:
0.275
Gnomad4 NFE
AF:
0.375
Gnomad4 OTH
AF:
0.468
Alfa
AF:
0.352
Hom.:
4304
Bravo
AF:
0.475

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
5.2
DANN
Benign
0.66

Splicing

Name
Calibrated prediction
Score
Prediction
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.

Other links and lift over

dbSNP: rs764533; hg19: chr7-23153875; API