2-231718803-A-G

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 0.116 in 152,276 control chromosomes in the GnomAD database, including 1,574 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 0.12 ( 1574 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.193
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=-0.73).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 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:
0.115
AC:
17568
AN:
152158
Hom.:
1573
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.247
Gnomad AMI
AF:
0.0669
Gnomad AMR
AF:
0.0757
Gnomad ASJ
AF:
0.0573
Gnomad EAS
AF:
0.0304
Gnomad SAS
AF:
0.111
Gnomad FIN
AF:
0.0488
Gnomad MID
AF:
0.0854
Gnomad NFE
AF:
0.0658
Gnomad OTH
AF:
0.102
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.116
AC:
17593
AN:
152276
Hom.:
1574
Cov.:
31
AF XY:
0.115
AC XY:
8542
AN XY:
74458
show subpopulations
Gnomad4 AFR
AF:
0.247
Gnomad4 AMR
AF:
0.0755
Gnomad4 ASJ
AF:
0.0573
Gnomad4 EAS
AF:
0.0304
Gnomad4 SAS
AF:
0.113
Gnomad4 FIN
AF:
0.0488
Gnomad4 NFE
AF:
0.0658
Gnomad4 OTH
AF:
0.100
Alfa
AF:
0.0749
Hom.:
677
Bravo
AF:
0.123
Asia WGS
AF:
0.0770
AC:
267
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.73
CADD
Benign
12
DANN
Benign
0.69

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: rs838436; hg19: chr2-232583513; API