chr6-32452402-C-T

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.162+7418G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 151,818 control chromosomes in the GnomAD database, including 24,808 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 0.57 ( 24808 hom., cov: 32)

Consequence

ENSG00000299747
ENST00000766007.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.12

Publications

35 publications found
Variant links:
Genes affected

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=-1.01).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.635 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
ENSG00000299747ENST00000766007.1 linkn.162+7418G>A intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.567
AC:
85956
AN:
151700
Hom.:
24796
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.486
Gnomad AMI
AF:
0.775
Gnomad AMR
AF:
0.646
Gnomad ASJ
AF:
0.732
Gnomad EAS
AF:
0.572
Gnomad SAS
AF:
0.635
Gnomad FIN
AF:
0.504
Gnomad MID
AF:
0.697
Gnomad NFE
AF:
0.589
Gnomad OTH
AF:
0.609
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.567
AC:
86008
AN:
151818
Hom.:
24808
Cov.:
32
AF XY:
0.566
AC XY:
42025
AN XY:
74196
show subpopulations
African (AFR)
AF:
0.486
AC:
20125
AN:
41382
American (AMR)
AF:
0.646
AC:
9848
AN:
15250
Ashkenazi Jewish (ASJ)
AF:
0.732
AC:
2539
AN:
3470
East Asian (EAS)
AF:
0.573
AC:
2960
AN:
5166
South Asian (SAS)
AF:
0.637
AC:
3072
AN:
4826
European-Finnish (FIN)
AF:
0.504
AC:
5297
AN:
10520
Middle Eastern (MID)
AF:
0.692
AC:
202
AN:
292
European-Non Finnish (NFE)
AF:
0.589
AC:
39990
AN:
67900
Other (OTH)
AF:
0.604
AC:
1273
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
1874
3749
5623
7498
9372
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
748
1496
2244
2992
3740
<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:
0.583
Hom.:
80818
Bravo
AF:
0.576
Asia WGS
AF:
0.542
AC:
1888
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
2.6
DANN
Benign
0.39
PhyloP100
-1.1

Splicing

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

Publications

Other links and lift over

dbSNP: rs7754768; hg19: chr6-32420179; COSMIC: COSV51803812; API