rs7739700

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 0.339 in 151,988 control chromosomes in the GnomAD database, including 9,212 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 0.34 ( 9212 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06
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=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 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:
0.339
AC:
51499
AN:
151872
Hom.:
9208
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.237
Gnomad AMI
AF:
0.441
Gnomad AMR
AF:
0.314
Gnomad ASJ
AF:
0.332
Gnomad EAS
AF:
0.470
Gnomad SAS
AF:
0.376
Gnomad FIN
AF:
0.380
Gnomad MID
AF:
0.411
Gnomad NFE
AF:
0.387
Gnomad OTH
AF:
0.325
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.339
AC:
51533
AN:
151988
Hom.:
9212
Cov.:
31
AF XY:
0.341
AC XY:
25343
AN XY:
74274
show subpopulations
Gnomad4 AFR
AF:
0.237
AC:
0.236939
AN:
0.236939
Gnomad4 AMR
AF:
0.314
AC:
0.314187
AN:
0.314187
Gnomad4 ASJ
AF:
0.332
AC:
0.332373
AN:
0.332373
Gnomad4 EAS
AF:
0.470
AC:
0.469779
AN:
0.469779
Gnomad4 SAS
AF:
0.376
AC:
0.375987
AN:
0.375987
Gnomad4 FIN
AF:
0.380
AC:
0.379568
AN:
0.379568
Gnomad4 NFE
AF:
0.387
AC:
0.387159
AN:
0.387159
Gnomad4 OTH
AF:
0.329
AC:
0.329234
AN:
0.329234
Heterozygous variant carriers
0
1683
3366
5048
6731
8414
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
510
1020
1530
2040
2550
<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:
0.271
Hom.:
1148
Bravo
AF:
0.328
Asia WGS
AF:
0.401
AC:
1391
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.84
DANN
Benign
0.74

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7739700; hg19: chr6-132954963; COSMIC: COSV58605478; API