14-54337047-T-C

Variant summary

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

The ENST00000770016.1(ENSG00000300202):​n.370-36870A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,090 control chromosomes in the GnomAD database, including 15,569 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 ( 15569 hom., cov: 33)

Consequence

ENSG00000300202
ENST00000770016.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.10

Publications

5 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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770016.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt

There are no transcript annotations for this variant.

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ENSG00000300202
ENST00000770016.1
n.370-36870A>G
intron
N/A
ENSG00000300202
ENST00000770017.1
n.410-36870A>G
intron
N/A
ENSG00000300202
ENST00000770018.1
n.522-36870A>G
intron
N/A

Frequencies

GnomAD3 genomes
AF:
0.429
AC:
65229
AN:
151972
Hom.:
15572
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.261
Gnomad AMI
AF:
0.549
Gnomad AMR
AF:
0.341
Gnomad ASJ
AF:
0.503
Gnomad EAS
AF:
0.183
Gnomad SAS
AF:
0.302
Gnomad FIN
AF:
0.560
Gnomad MID
AF:
0.490
Gnomad NFE
AF:
0.553
Gnomad OTH
AF:
0.443
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.429
AC:
65218
AN:
152090
Hom.:
15569
Cov.:
33
AF XY:
0.424
AC XY:
31552
AN XY:
74348
show subpopulations
African (AFR)
AF:
0.261
AC:
10809
AN:
41482
American (AMR)
AF:
0.340
AC:
5198
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.503
AC:
1744
AN:
3470
East Asian (EAS)
AF:
0.183
AC:
948
AN:
5176
South Asian (SAS)
AF:
0.302
AC:
1458
AN:
4820
European-Finnish (FIN)
AF:
0.560
AC:
5923
AN:
10572
Middle Eastern (MID)
AF:
0.476
AC:
139
AN:
292
European-Non Finnish (NFE)
AF:
0.553
AC:
37573
AN:
67980
Other (OTH)
AF:
0.438
AC:
925
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1778
3555
5333
7110
8888
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
602
1204
1806
2408
3010
<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:
0.505
Hom.:
66843
Bravo
AF:
0.404
Asia WGS
AF:
0.241
AC:
838
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.0080
DANN
Benign
0.78
PhyloP100
-2.1

Splicing

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

Publications

Other links and lift over

dbSNP: rs10150369; hg19: chr14-54803765; API