GeneBe

12-52632782-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000550729.2(KRT128P):​n.663+84A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,616 control chromosomes in the GnomAD database, including 7,758 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 0.31 ( 7740 hom., cov: 33)
Exomes 𝑓: 0.31 ( 18 hom. )

Consequence

KRT128P
ENST00000550729.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.512
Variant links:
Genes affected
KRT128P (HGNC:48882): (keratin 128, pseudogene)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KRT128PENST00000550729.2 linkn.663+84A>G intron_variant Intron 3 of 6 6

Frequencies

GnomAD3 genomes
AF:
0.309
AC:
47040
AN:
152044
Hom.:
7731
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.412
Gnomad AMI
AF:
0.449
Gnomad AMR
AF:
0.320
Gnomad ASJ
AF:
0.219
Gnomad EAS
AF:
0.224
Gnomad SAS
AF:
0.329
Gnomad FIN
AF:
0.298
Gnomad MID
AF:
0.206
Gnomad NFE
AF:
0.256
Gnomad OTH
AF:
0.284
GnomAD4 exome
AF:
0.313
AC:
142
AN:
454
Hom.:
18
AF XY:
0.333
AC XY:
92
AN XY:
276
show subpopulations
African (AFR)
AF:
0.500
AC:
1
AN:
2
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
0.500
AC:
1
AN:
2
South Asian (SAS)
AF:
0.500
AC:
1
AN:
2
European-Finnish (FIN)
AF:
0.299
AC:
125
AN:
418
Middle Eastern (MID)
AF:
0.500
AC:
1
AN:
2
European-Non Finnish (NFE)
AF:
0.500
AC:
12
AN:
24
Other (OTH)
AF:
0.250
AC:
1
AN:
4
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.508
Heterozygous variant carriers
0
6
12
19
25
31
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.309
AC:
47082
AN:
152162
Hom.:
7740
Cov.:
33
AF XY:
0.311
AC XY:
23107
AN XY:
74404
show subpopulations
African (AFR)
AF:
0.411
AC:
17068
AN:
41484
American (AMR)
AF:
0.319
AC:
4885
AN:
15300
Ashkenazi Jewish (ASJ)
AF:
0.219
AC:
759
AN:
3472
East Asian (EAS)
AF:
0.224
AC:
1161
AN:
5180
South Asian (SAS)
AF:
0.329
AC:
1583
AN:
4816
European-Finnish (FIN)
AF:
0.298
AC:
3159
AN:
10598
Middle Eastern (MID)
AF:
0.207
AC:
61
AN:
294
European-Non Finnish (NFE)
AF:
0.256
AC:
17394
AN:
67994
Other (OTH)
AF:
0.285
AC:
603
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1654
3308
4962
6616
8270
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
466
932
1398
1864
2330
<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:
0.286
Hom.:
763
Bravo
AF:
0.314
Asia WGS
AF:
0.299
AC:
1039
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
4.4
DANN
Benign
0.78
PhyloP100
-0.51

Splicing

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

Publications

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Other links and lift over

dbSNP: rs626758; hg19: chr12-53026566; COSMIC: COSV73574037; API