GeneBe

chr20-49957917-G-T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000422599.1(KRT18P4):​n.1173G>T 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 0.00000929 in 753,176 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000026 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0000050 ( 0 hom. )

Consequence

KRT18P4
ENST00000422599.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.33

Publications

5 publications found
Variant links:
Genes affected
KRT18P4 (HGNC:16604): (keratin 18 pseudogene 4)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KRT18P4 n.49957917G>T intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KRT18P4ENST00000422599.1 linkn.1173G>T non_coding_transcript_exon_variant Exon 1 of 1 6

Frequencies

GnomAD3 genomes
AF:
0.0000264
AC:
4
AN:
151792
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0000725
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000657
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000499
AC:
3
AN:
601384
Hom.:
0
Cov.:
5
AF XY:
0.00000306
AC XY:
1
AN XY:
327292
show subpopulations
African (AFR)
AF:
0.000114
AC:
2
AN:
17562
American (AMR)
AF:
0.0000247
AC:
1
AN:
40452
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
20584
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35440
South Asian (SAS)
AF:
0.00
AC:
0
AN:
67632
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
35952
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2510
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
349018
Other (OTH)
AF:
0.00
AC:
0
AN:
32234
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.0000264
AC:
4
AN:
151792
Hom.:
0
Cov.:
30
AF XY:
0.0000270
AC XY:
2
AN XY:
74082
show subpopulations
African (AFR)
AF:
0.0000725
AC:
3
AN:
41364
American (AMR)
AF:
0.0000657
AC:
1
AN:
15212
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3468
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5164
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4802
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10542
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
67932
Other (OTH)
AF:
0.00
AC:
0
AN:
2080
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.563
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.00
Hom.:
813

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
CADD
Benign
6.8
DANN
Benign
0.93
PhyloP100
1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs6067284; hg19: chr20-48574454; API