rs2107595

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.193 in 151,892 control chromosomes in the GnomAD database, including 2,975 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 0.19 ( 2975 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.65
Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 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:
0.193
AC:
29224
AN:
151774
Hom.:
2958
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.208
Gnomad AMI
AF:
0.126
Gnomad AMR
AF:
0.199
Gnomad ASJ
AF:
0.234
Gnomad EAS
AF:
0.337
Gnomad SAS
AF:
0.308
Gnomad FIN
AF:
0.204
Gnomad MID
AF:
0.218
Gnomad NFE
AF:
0.159
Gnomad OTH
AF:
0.192
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.193
AC:
29266
AN:
151892
Hom.:
2975
Cov.:
33
AF XY:
0.196
AC XY:
14549
AN XY:
74244
show subpopulations
Gnomad4 AFR
AF:
0.208
Gnomad4 AMR
AF:
0.199
Gnomad4 ASJ
AF:
0.234
Gnomad4 EAS
AF:
0.337
Gnomad4 SAS
AF:
0.308
Gnomad4 FIN
AF:
0.204
Gnomad4 NFE
AF:
0.159
Gnomad4 OTH
AF:
0.202
Alfa
AF:
0.171
Hom.:
1846
Bravo
AF:
0.193
Asia WGS
AF:
0.339
AC:
1177
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.43
CADD
Benign
18
DANN
Benign
0.64

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: rs2107595; hg19: chr7-19049388; API