rs1930713

Variant summary

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

The ENST00000665764.1(ENSG00000285082):​n.*17-665G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,194 control chromosomes in the GnomAD database, including 4,217 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 0.23 ( 4217 hom., cov: 33)

Consequence

ENSG00000285082
ENST00000665764.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.224

Publications

3 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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.244 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
ENSG00000285082ENST00000665764.1 linkn.*17-665G>A intron_variant Intron 2 of 6 ENSP00000499745.1 A0A2R8YGN2
ENSG00000285082ENST00000697636.1 linkn.*17-85596G>A intron_variant Intron 2 of 5 ENSP00000513366.1 A0A2R8YGN2
ENSG00000284977ENST00000697639.1 linkn.1054-85596G>A intron_variant Intron 7 of 12

Frequencies

GnomAD3 genomes
AF:
0.228
AC:
34731
AN:
152076
Hom.:
4211
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.222
Gnomad AMI
AF:
0.169
Gnomad AMR
AF:
0.208
Gnomad ASJ
AF:
0.383
Gnomad EAS
AF:
0.0384
Gnomad SAS
AF:
0.180
Gnomad FIN
AF:
0.222
Gnomad MID
AF:
0.316
Gnomad NFE
AF:
0.248
Gnomad OTH
AF:
0.243
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.228
AC:
34758
AN:
152194
Hom.:
4217
Cov.:
33
AF XY:
0.226
AC XY:
16789
AN XY:
74422
show subpopulations
African (AFR)
AF:
0.222
AC:
9229
AN:
41530
American (AMR)
AF:
0.207
AC:
3173
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
0.383
AC:
1328
AN:
3468
East Asian (EAS)
AF:
0.0383
AC:
198
AN:
5176
South Asian (SAS)
AF:
0.182
AC:
881
AN:
4828
European-Finnish (FIN)
AF:
0.222
AC:
2355
AN:
10594
Middle Eastern (MID)
AF:
0.310
AC:
91
AN:
294
European-Non Finnish (NFE)
AF:
0.248
AC:
16830
AN:
67986
Other (OTH)
AF:
0.246
AC:
519
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1400
2801
4201
5602
7002
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
364
728
1092
1456
1820
<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:
0.242
Hom.:
19579
Bravo
AF:
0.227
Asia WGS
AF:
0.115
AC:
401
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.3
DANN
Benign
0.58
PhyloP100
0.22

Splicing

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

Publications

Other links and lift over

dbSNP: rs1930713; hg19: chr9-120733712; API