rs649446

Variant summary

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

The ENST00000660751.1(ENSG00000287425):​n.1352C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,146 control chromosomes in the GnomAD database, including 3,699 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 0.22 ( 3699 hom., cov: 32)

Consequence

ENSG00000287425
ENST00000660751.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.695

Publications

8 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=-0.68).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 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
ENSG00000287425ENST00000660751.1 linkn.1352C>T non_coding_transcript_exon_variant Exon 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.216
AC:
32879
AN:
152026
Hom.:
3699
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.269
Gnomad AMI
AF:
0.162
Gnomad AMR
AF:
0.174
Gnomad ASJ
AF:
0.212
Gnomad EAS
AF:
0.285
Gnomad SAS
AF:
0.235
Gnomad FIN
AF:
0.206
Gnomad MID
AF:
0.161
Gnomad NFE
AF:
0.190
Gnomad OTH
AF:
0.214
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.216
AC:
32899
AN:
152146
Hom.:
3699
Cov.:
32
AF XY:
0.218
AC XY:
16200
AN XY:
74370
show subpopulations
African (AFR)
AF:
0.269
AC:
11146
AN:
41484
American (AMR)
AF:
0.174
AC:
2661
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
0.212
AC:
734
AN:
3468
East Asian (EAS)
AF:
0.285
AC:
1476
AN:
5178
South Asian (SAS)
AF:
0.234
AC:
1129
AN:
4820
European-Finnish (FIN)
AF:
0.206
AC:
2184
AN:
10582
Middle Eastern (MID)
AF:
0.163
AC:
48
AN:
294
European-Non Finnish (NFE)
AF:
0.190
AC:
12924
AN:
68010
Other (OTH)
AF:
0.212
AC:
449
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1308
2616
3923
5231
6539
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
346
692
1038
1384
1730
<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:
0.204
Hom.:
3890
Bravo
AF:
0.215
Asia WGS
AF:
0.239
AC:
831
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
3.6
DANN
Benign
0.80
PhyloP100
-0.69

Splicing

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

Publications

Other links and lift over

dbSNP: rs649446; hg19: chr11-73695845; API