rs2307930

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.187 in 152,106 control chromosomes in the GnomAD database, including 3,161 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.19 ( 3161 hom., cov: 28)

Consequence

Unknown

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.512
Variant links:

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ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.187
AC:
28454
AN:
151988
Hom.:
3154
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.142
Gnomad AMI
AF:
0.137
Gnomad AMR
AF:
0.315
Gnomad ASJ
AF:
0.218
Gnomad EAS
AF:
0.467
Gnomad SAS
AF:
0.226
Gnomad FIN
AF:
0.139
Gnomad MID
AF:
0.190
Gnomad NFE
AF:
0.168
Gnomad OTH
AF:
0.210
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.187
AC:
28474
AN:
152106
Hom.:
3161
Cov.:
28
AF XY:
0.190
AC XY:
14135
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.142
Gnomad4 AMR
AF:
0.316
Gnomad4 ASJ
AF:
0.218
Gnomad4 EAS
AF:
0.467
Gnomad4 SAS
AF:
0.227
Gnomad4 FIN
AF:
0.139
Gnomad4 NFE
AF:
0.168
Gnomad4 OTH
AF:
0.209
Alfa
AF:
0.168
Hom.:
249
Bravo
AF:
0.199
Asia WGS
AF:
0.300
AC:
1045
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs2307930; hg19: chr6-84476378; API