GeneBe

chr2-75199842-T-A

Variant names:

Variant summary

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

The NR_168009.1(TACR1-AS1):​n.372+43527T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,568 control chromosomes in the GnomAD database, including 3,105 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 0.18 ( 3096 hom., cov: 32)
Exomes 𝑓: 0.20 ( 9 hom. )

Consequence

TACR1-AS1
NR_168009.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18

Publications

2 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=-0.63).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TACR1-AS1NR_168009.1 linkn.372+43527T>A intron_variant Intron 2 of 3
TACR1-AS1NR_168010.1 linkn.366+43527T>A intron_variant Intron 2 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.183
AC:
27755
AN:
152026
Hom.:
3100
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0612
Gnomad AMI
AF:
0.152
Gnomad AMR
AF:
0.249
Gnomad ASJ
AF:
0.199
Gnomad EAS
AF:
0.0746
Gnomad SAS
AF:
0.114
Gnomad FIN
AF:
0.215
Gnomad MID
AF:
0.241
Gnomad NFE
AF:
0.248
Gnomad OTH
AF:
0.210
GnomAD4 exome
AF:
0.198
AC:
84
AN:
424
Hom.:
9
AF XY:
0.198
AC XY:
67
AN XY:
338
show subpopulations
African (AFR)
AF:
0.100
AC:
1
AN:
10
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2
East Asian (EAS)
AF:
0.00
AC:
0
AN:
8
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2
European-Finnish (FIN)
AF:
0.211
AC:
8
AN:
38
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2
European-Non Finnish (NFE)
AF:
0.206
AC:
66
AN:
320
Other (OTH)
AF:
0.214
AC:
9
AN:
42
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
4
7
11
14
18
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.182
AC:
27752
AN:
152144
Hom.:
3096
Cov.:
32
AF XY:
0.181
AC XY:
13435
AN XY:
74356
show subpopulations
African (AFR)
AF:
0.0611
AC:
2539
AN:
41554
American (AMR)
AF:
0.249
AC:
3809
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.199
AC:
688
AN:
3464
East Asian (EAS)
AF:
0.0749
AC:
386
AN:
5152
South Asian (SAS)
AF:
0.114
AC:
548
AN:
4816
European-Finnish (FIN)
AF:
0.215
AC:
2273
AN:
10588
Middle Eastern (MID)
AF:
0.245
AC:
72
AN:
294
European-Non Finnish (NFE)
AF:
0.248
AC:
16858
AN:
67962
Other (OTH)
AF:
0.209
AC:
440
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1129
2258
3388
4517
5646
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
290
580
870
1160
1450
<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:
0.206
Hom.:
470
Bravo
AF:
0.182
Asia WGS
AF:
0.117
AC:
410
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.63
CADD
Benign
14
DANN
Benign
0.84
PhyloP100
1.2
PromoterAI
-0.12
Neutral

Splicing

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

Publications

Other links and lift over

dbSNP: rs2193405; hg19: chr2-75426968; API