rs3825295

Variant summary

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

The NM_001199805.1(KLRC4-KLRK1):​c.-488+23T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 99,908 control chromosomes in the GnomAD database, including 715 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 0.10 ( 714 hom., cov: 28)
Exomes 𝑓: 0.039 ( 1 hom. )

Consequence

KLRC4-KLRK1
NM_001199805.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.505
Variant links:
Genes affected
KLRC4-KLRK1 (HGNC:48357): (KLRC4-KLRK1 readthrough) This locus represents naturally occurring read-through transcription between the neighboring KLRC4 (killer cell lectin-like receptor subfamily C, member 4) and KLRK1 (killer cell lectin-like receptor subfamily K, member 1) genes on chromosome 12. The read-through transcript includes an alternate 5' exon and lacks a significant portion of the KLRC4 coding sequence, including the start codon, and it thus encodes the KLRK1 protein. [provided by RefSeq, Dec 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=-0.83).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KLRC4-KLRK1NM_001199805.1 linkuse as main transcriptc.-488+23T>C intron_variant NP_001186734.1 P26718-1A0A024RAP8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KLRC4-KLRK1ENST00000543812.5 linkuse as main transcriptn.-63+23T>C intron_variant 2 ENSP00000457500.1 H3BU71
KLRC4-KLRK1ENST00000585507.5 linkuse as main transcriptn.-63+23T>C intron_variant 5 ENSP00000465434.1 H3BU71
KLRC4-KLRK1ENST00000588263.5 linkuse as main transcriptn.-153+23T>C intron_variant 5 ENSP00000468074.1 H3BU71

Frequencies

GnomAD3 genomes
AF:
0.102
AC:
10177
AN:
99680
Hom.:
712
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.143
Gnomad AMI
AF:
0.00190
Gnomad AMR
AF:
0.187
Gnomad ASJ
AF:
0.0214
Gnomad EAS
AF:
0.261
Gnomad SAS
AF:
0.390
Gnomad FIN
AF:
0.0701
Gnomad MID
AF:
0.0481
Gnomad NFE
AF:
0.00870
Gnomad OTH
AF:
0.0747
GnomAD4 exome
AF:
0.0391
AC:
5
AN:
128
Hom.:
1
Cov.:
0
AF XY:
0.0465
AC XY:
4
AN XY:
86
show subpopulations
Gnomad4 AFR exome
AF:
0.500
Gnomad4 AMR exome
AF:
1.00
Gnomad4 EAS exome
AF:
0.500
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.167
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.102
AC:
10194
AN:
99780
Hom.:
714
Cov.:
28
AF XY:
0.111
AC XY:
5393
AN XY:
48780
show subpopulations
Gnomad4 AFR
AF:
0.143
Gnomad4 AMR
AF:
0.187
Gnomad4 ASJ
AF:
0.0214
Gnomad4 EAS
AF:
0.261
Gnomad4 SAS
AF:
0.389
Gnomad4 FIN
AF:
0.0701
Gnomad4 NFE
AF:
0.00876
Gnomad4 OTH
AF:
0.0766
Alfa
AF:
0.0426
Hom.:
49
Bravo
AF:
0.0730

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
4.9
DANN
Benign
0.30

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.

Other links and lift over

dbSNP: rs3825295; hg19: chr12-10562675; API