rs2205187

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.236 in 152,114 control chromosomes in the GnomAD database, including 4,570 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 0.24 ( 4570 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.719
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 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:
0.236
AC:
35820
AN:
151996
Hom.:
4563
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.337
Gnomad AMI
AF:
0.179
Gnomad AMR
AF:
0.199
Gnomad ASJ
AF:
0.195
Gnomad EAS
AF:
0.0965
Gnomad SAS
AF:
0.145
Gnomad FIN
AF:
0.200
Gnomad MID
AF:
0.231
Gnomad NFE
AF:
0.207
Gnomad OTH
AF:
0.238
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.236
AC:
35834
AN:
152114
Hom.:
4570
Cov.:
32
AF XY:
0.231
AC XY:
17197
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.337
Gnomad4 AMR
AF:
0.199
Gnomad4 ASJ
AF:
0.195
Gnomad4 EAS
AF:
0.0967
Gnomad4 SAS
AF:
0.146
Gnomad4 FIN
AF:
0.200
Gnomad4 NFE
AF:
0.207
Gnomad4 OTH
AF:
0.235
Alfa
AF:
0.215
Hom.:
654
Bravo
AF:
0.240
Asia WGS
AF:
0.121
AC:
423
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.42
DANN
Benign
0.44

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: rs2205187; hg19: chr14-75841212; API