rs3868143

Variant summary

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

The NM_001100915.3(KCTD19):​c.1590+30A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 1,494,894 control chromosomes in the GnomAD database, including 18,837 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 0.22 ( 7686 hom., cov: 32)
Exomes 𝑓: 0.094 ( 11151 hom. )

Consequence

KCTD19
NM_001100915.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.02
Variant links:
Genes affected
KCTD19 (HGNC:24753): (potassium channel tetramerization domain containing 19) Predicted to be involved in protein homooligomerization. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KCTD19NM_001100915.3 linkuse as main transcriptc.1590+30A>G intron_variant ENST00000304372.6 NP_001094385.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KCTD19ENST00000304372.6 linkuse as main transcriptc.1590+30A>G intron_variant 1 NM_001100915.3 ENSP00000305702 P1
KCTD19ENST00000570049.5 linkuse as main transcriptn.3422+30A>G intron_variant, non_coding_transcript_variant 1
KCTD19ENST00000566392.5 linkuse as main transcriptn.2859+30A>G intron_variant, non_coding_transcript_variant 2
KCTD19ENST00000569333.5 linkuse as main transcriptn.3588+30A>G intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.223
AC:
33856
AN:
152024
Hom.:
7649
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.584
Gnomad AMI
AF:
0.0760
Gnomad AMR
AF:
0.113
Gnomad ASJ
AF:
0.0608
Gnomad EAS
AF:
0.00481
Gnomad SAS
AF:
0.143
Gnomad FIN
AF:
0.147
Gnomad MID
AF:
0.184
Gnomad NFE
AF:
0.0740
Gnomad OTH
AF:
0.169
GnomAD3 exomes
AF:
0.119
AC:
29444
AN:
248402
Hom.:
3866
AF XY:
0.115
AC XY:
15484
AN XY:
134778
show subpopulations
Gnomad AFR exome
AF:
0.595
Gnomad AMR exome
AF:
0.0659
Gnomad ASJ exome
AF:
0.0687
Gnomad EAS exome
AF:
0.00390
Gnomad SAS exome
AF:
0.157
Gnomad FIN exome
AF:
0.141
Gnomad NFE exome
AF:
0.0786
Gnomad OTH exome
AF:
0.0960
GnomAD4 exome
AF:
0.0940
AC:
126188
AN:
1342752
Hom.:
11151
Cov.:
21
AF XY:
0.0937
AC XY:
63172
AN XY:
674108
show subpopulations
Gnomad4 AFR exome
AF:
0.608
Gnomad4 AMR exome
AF:
0.0699
Gnomad4 ASJ exome
AF:
0.0714
Gnomad4 EAS exome
AF:
0.00263
Gnomad4 SAS exome
AF:
0.148
Gnomad4 FIN exome
AF:
0.140
Gnomad4 NFE exome
AF:
0.0747
Gnomad4 OTH exome
AF:
0.115
GnomAD4 genome
AF:
0.223
AC:
33939
AN:
152142
Hom.:
7686
Cov.:
32
AF XY:
0.221
AC XY:
16466
AN XY:
74378
show subpopulations
Gnomad4 AFR
AF:
0.584
Gnomad4 AMR
AF:
0.112
Gnomad4 ASJ
AF:
0.0608
Gnomad4 EAS
AF:
0.00482
Gnomad4 SAS
AF:
0.143
Gnomad4 FIN
AF:
0.147
Gnomad4 NFE
AF:
0.0740
Gnomad4 OTH
AF:
0.167
Alfa
AF:
0.110
Hom.:
1315
Bravo
AF:
0.233
Asia WGS
AF:
0.124
AC:
433
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.36
DANN
Benign
0.38

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: rs3868143; hg19: chr16-67328453; COSMIC: COSV58572555; COSMIC: COSV58572555; API