chr6-140757642-G-C

Variant summary

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

The ENST00000650553.2(ENSG00000234147):​n.293+58490C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,000 control chromosomes in the GnomAD database, including 15,791 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 0.43 ( 15791 hom., cov: 32)

Consequence

ENSG00000234147
ENST00000650553.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0920

Publications

0 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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105378027XR_001744385.2 linkn.1307-253G>C intron_variant Intron 4 of 8
LOC105378027XR_001744387.3 linkn.1307-253G>C intron_variant Intron 4 of 7
LOC105378027XR_001744388.2 linkn.1209-253G>C intron_variant Intron 3 of 7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000234147ENST00000650553.2 linkn.293+58490C>G intron_variant Intron 2 of 4
ENSG00000288714ENST00000682976.1 linkn.327-253G>C intron_variant Intron 2 of 2
ENSG00000288714ENST00000684511.1 linkn.595-253G>C intron_variant Intron 5 of 8

Frequencies

GnomAD3 genomes
AF:
0.430
AC:
65316
AN:
151882
Hom.:
15751
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.660
Gnomad AMI
AF:
0.424
Gnomad AMR
AF:
0.336
Gnomad ASJ
AF:
0.339
Gnomad EAS
AF:
0.330
Gnomad SAS
AF:
0.400
Gnomad FIN
AF:
0.347
Gnomad MID
AF:
0.399
Gnomad NFE
AF:
0.339
Gnomad OTH
AF:
0.408
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.430
AC:
65412
AN:
152000
Hom.:
15791
Cov.:
32
AF XY:
0.426
AC XY:
31633
AN XY:
74278
show subpopulations
African (AFR)
AF:
0.660
AC:
27356
AN:
41464
American (AMR)
AF:
0.337
AC:
5137
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
0.339
AC:
1176
AN:
3464
East Asian (EAS)
AF:
0.331
AC:
1707
AN:
5162
South Asian (SAS)
AF:
0.399
AC:
1920
AN:
4816
European-Finnish (FIN)
AF:
0.347
AC:
3660
AN:
10534
Middle Eastern (MID)
AF:
0.401
AC:
118
AN:
294
European-Non Finnish (NFE)
AF:
0.339
AC:
23080
AN:
67988
Other (OTH)
AF:
0.414
AC:
872
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1756
3511
5267
7022
8778
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
596
1192
1788
2384
2980
<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:
0.380
Hom.:
1558
Bravo
AF:
0.442
Asia WGS
AF:
0.426
AC:
1485
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.58
DANN
Benign
0.40
PhyloP100
-0.092

Splicing

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

Publications

Other links and lift over

dbSNP: rs1568483; hg19: chr6-141078779; COSMIC: COSV68356889; API