rs2242547

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 0.0403 in 151,890 control chromosomes in the GnomAD database, including 250 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 0.040 ( 250 hom., cov: 28)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.224
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=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0997 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:
0.0404
AC:
6125
AN:
151772
Hom.:
250
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.102
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0261
Gnomad ASJ
AF:
0.00288
Gnomad EAS
AF:
0.0360
Gnomad SAS
AF:
0.0709
Gnomad FIN
AF:
0.00482
Gnomad MID
AF:
0.0380
Gnomad NFE
AF:
0.0122
Gnomad OTH
AF:
0.0359
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0403
AC:
6126
AN:
151890
Hom.:
250
Cov.:
28
AF XY:
0.0410
AC XY:
3048
AN XY:
74272
show subpopulations
Gnomad4 AFR
AF:
0.102
Gnomad4 AMR
AF:
0.0261
Gnomad4 ASJ
AF:
0.00288
Gnomad4 EAS
AF:
0.0359
Gnomad4 SAS
AF:
0.0703
Gnomad4 FIN
AF:
0.00482
Gnomad4 NFE
AF:
0.0122
Gnomad4 OTH
AF:
0.0355
Alfa
AF:
0.0261
Hom.:
48
Bravo
AF:
0.0433
Asia WGS
AF:
0.0530
AC:
184
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
6.0
DANN
Benign
0.56

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: rs2242547; hg19: chr14-22963305; API