GeneBe

rs1634514

Variant names:

Variant summary

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

The variant allele was found at a frequency of 0.196 in 329,076 control chromosomes in the GnomAD database, including 7,143 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 ( 2834 hom., cov: 30)
Exomes 𝑓: 0.21 ( 4309 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.172

Publications

4 publications found
Variant links:

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ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 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

Frequencies

GnomAD3 genomes
AF:
0.179
AC:
27071
AN:
151598
Hom.:
2833
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0717
Gnomad AMI
AF:
0.297
Gnomad AMR
AF:
0.189
Gnomad ASJ
AF:
0.155
Gnomad EAS
AF:
0.300
Gnomad SAS
AF:
0.224
Gnomad FIN
AF:
0.157
Gnomad MID
AF:
0.180
Gnomad NFE
AF:
0.232
Gnomad OTH
AF:
0.184
GnomAD4 exome
AF:
0.210
AC:
37268
AN:
177360
Hom.:
4309
AF XY:
0.209
AC XY:
20001
AN XY:
95494
show subpopulations
African (AFR)
AF:
0.0667
AC:
368
AN:
5516
American (AMR)
AF:
0.191
AC:
1508
AN:
7878
Ashkenazi Jewish (ASJ)
AF:
0.171
AC:
776
AN:
4534
East Asian (EAS)
AF:
0.285
AC:
2287
AN:
8034
South Asian (SAS)
AF:
0.204
AC:
6284
AN:
30774
European-Finnish (FIN)
AF:
0.160
AC:
1292
AN:
8076
Middle Eastern (MID)
AF:
0.167
AC:
112
AN:
670
European-Non Finnish (NFE)
AF:
0.222
AC:
22845
AN:
102770
Other (OTH)
AF:
0.197
AC:
1796
AN:
9108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.491
Heterozygous variant carriers
0
1325
2651
3976
5302
6627
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
174
348
522
696
870
<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:
0.178
AC:
27077
AN:
151716
Hom.:
2834
Cov.:
30
AF XY:
0.176
AC XY:
13065
AN XY:
74098
show subpopulations
African (AFR)
AF:
0.0719
AC:
2981
AN:
41450
American (AMR)
AF:
0.188
AC:
2864
AN:
15226
Ashkenazi Jewish (ASJ)
AF:
0.155
AC:
537
AN:
3460
East Asian (EAS)
AF:
0.299
AC:
1537
AN:
5142
South Asian (SAS)
AF:
0.225
AC:
1062
AN:
4720
European-Finnish (FIN)
AF:
0.157
AC:
1660
AN:
10560
Middle Eastern (MID)
AF:
0.194
AC:
57
AN:
294
European-Non Finnish (NFE)
AF:
0.232
AC:
15726
AN:
67846
Other (OTH)
AF:
0.182
AC:
383
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1051
2102
3153
4204
5255
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
294
588
882
1176
1470
<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:
0.199
Hom.:
415
Bravo
AF:
0.179

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
2.3
DANN
Benign
0.76
PhyloP100
0.17
PromoterAI
0.0034
Neutral

Splicing

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

Publications

Other links and lift over

dbSNP: rs1634514; hg19: chr17-34430918; API