rs2267864

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 0.199 in 158,766 control chromosomes in the GnomAD database, including 3,232 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 0.20 ( 3115 hom., cov: 32)
Exomes 𝑓: 0.16 ( 117 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.577
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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 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:
0.201
AC:
30476
AN:
151766
Hom.:
3102
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.220
Gnomad AMI
AF:
0.316
Gnomad AMR
AF:
0.200
Gnomad ASJ
AF:
0.204
Gnomad EAS
AF:
0.101
Gnomad SAS
AF:
0.154
Gnomad FIN
AF:
0.235
Gnomad MID
AF:
0.244
Gnomad NFE
AF:
0.193
Gnomad OTH
AF:
0.204
GnomAD4 exome
AF:
0.163
AC:
1122
AN:
6882
Hom.:
117
AF XY:
0.168
AC XY:
621
AN XY:
3692
show subpopulations
Gnomad4 AFR exome
AF:
0.182
Gnomad4 AMR exome
AF:
0.160
Gnomad4 ASJ exome
AF:
0.0909
Gnomad4 EAS exome
AF:
0.103
Gnomad4 SAS exome
AF:
0.160
Gnomad4 FIN exome
AF:
0.200
Gnomad4 NFE exome
AF:
0.167
Gnomad4 OTH exome
AF:
0.162
GnomAD4 genome
AF:
0.201
AC:
30540
AN:
151884
Hom.:
3115
Cov.:
32
AF XY:
0.204
AC XY:
15110
AN XY:
74216
show subpopulations
Gnomad4 AFR
AF:
0.220
Gnomad4 AMR
AF:
0.200
Gnomad4 ASJ
AF:
0.204
Gnomad4 EAS
AF:
0.101
Gnomad4 SAS
AF:
0.156
Gnomad4 FIN
AF:
0.235
Gnomad4 NFE
AF:
0.193
Gnomad4 OTH
AF:
0.207
Alfa
AF:
0.0981
Hom.:
137
Bravo
AF:
0.200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
4.5
DANN
Benign
0.43

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: rs2267864; hg19: chr20-43805279; API