rs2318308

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 0.344 in 151,706 control chromosomes in the GnomAD database, including 9,669 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 0.34 ( 9669 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.335
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=-1.06).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 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:
0.344
AC:
52166
AN:
151588
Hom.:
9646
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.472
Gnomad AMI
AF:
0.345
Gnomad AMR
AF:
0.368
Gnomad ASJ
AF:
0.332
Gnomad EAS
AF:
0.272
Gnomad SAS
AF:
0.270
Gnomad FIN
AF:
0.251
Gnomad MID
AF:
0.342
Gnomad NFE
AF:
0.287
Gnomad OTH
AF:
0.338
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.344
AC:
52239
AN:
151706
Hom.:
9669
Cov.:
30
AF XY:
0.343
AC XY:
25469
AN XY:
74152
show subpopulations
Gnomad4 AFR
AF:
0.472
Gnomad4 AMR
AF:
0.368
Gnomad4 ASJ
AF:
0.332
Gnomad4 EAS
AF:
0.272
Gnomad4 SAS
AF:
0.269
Gnomad4 FIN
AF:
0.251
Gnomad4 NFE
AF:
0.287
Gnomad4 OTH
AF:
0.338
Alfa
AF:
0.301
Hom.:
10454
Bravo
AF:
0.361
Asia WGS
AF:
0.321
AC:
1117
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
0.28
DANN
Benign
0.49

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: rs2318308; hg19: chr14-66391099; API