GeneBe

rs1401

Variant names:

Variant summary

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

The ENST00000623089.1(ENSG00000279810):​n.253C>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 0.243 in 152,142 control chromosomes in the GnomAD database, including 5,429 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 0.24 ( 5428 hom., cov: 31)
Exomes 𝑓: 0.31 ( 1 hom. )

Consequence

ENSG00000279810
ENST00000623089.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.305

Publications

7 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=-0.91).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.352 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
ENSG00000279810ENST00000623089.1 linkn.253C>T non_coding_transcript_exon_variant Exon 1 of 1 6

Frequencies

GnomAD3 genomes
AF:
0.244
AC:
37018
AN:
152000
Hom.:
5426
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0764
Gnomad AMI
AF:
0.250
Gnomad AMR
AF:
0.359
Gnomad ASJ
AF:
0.259
Gnomad EAS
AF:
0.203
Gnomad SAS
AF:
0.303
Gnomad FIN
AF:
0.263
Gnomad MID
AF:
0.278
Gnomad NFE
AF:
0.313
Gnomad OTH
AF:
0.274
GnomAD4 exome
AF:
0.308
AC:
8
AN:
26
Hom.:
1
Cov.:
0
AF XY:
0.227
AC XY:
5
AN XY:
22
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.333
AC:
8
AN:
24
Other (OTH)
AF:
0.00
AC:
0
AN:
2
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.492
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.243
AC:
37036
AN:
152116
Hom.:
5428
Cov.:
31
AF XY:
0.243
AC XY:
18097
AN XY:
74328
show subpopulations
African (AFR)
AF:
0.0762
AC:
3166
AN:
41532
American (AMR)
AF:
0.359
AC:
5495
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.259
AC:
900
AN:
3472
East Asian (EAS)
AF:
0.204
AC:
1051
AN:
5158
South Asian (SAS)
AF:
0.303
AC:
1458
AN:
4810
European-Finnish (FIN)
AF:
0.263
AC:
2780
AN:
10570
Middle Eastern (MID)
AF:
0.286
AC:
84
AN:
294
European-Non Finnish (NFE)
AF:
0.313
AC:
21296
AN:
67970
Other (OTH)
AF:
0.274
AC:
578
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1328
2655
3983
5310
6638
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
396
792
1188
1584
1980
<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:
0.272
Hom.:
1000
Bravo
AF:
0.241
Asia WGS
AF:
0.241
AC:
834
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.5
DANN
Benign
0.53
PhyloP100
0.30

Splicing

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

Publications

Other links and lift over

dbSNP: rs1401; hg19: chr6-169433728; COSMIC: COSV69502670; API