rs3848711

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 0.508 in 152,098 control chromosomes in the GnomAD database, including 20,229 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 0.51 ( 20229 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.462
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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.566 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:
0.508
AC:
77247
AN:
151980
Hom.:
20210
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.386
Gnomad AMI
AF:
0.572
Gnomad AMR
AF:
0.534
Gnomad ASJ
AF:
0.410
Gnomad EAS
AF:
0.526
Gnomad SAS
AF:
0.431
Gnomad FIN
AF:
0.603
Gnomad MID
AF:
0.494
Gnomad NFE
AF:
0.571
Gnomad OTH
AF:
0.514
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.508
AC:
77297
AN:
152098
Hom.:
20229
Cov.:
33
AF XY:
0.507
AC XY:
37723
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.386
Gnomad4 AMR
AF:
0.534
Gnomad4 ASJ
AF:
0.410
Gnomad4 EAS
AF:
0.526
Gnomad4 SAS
AF:
0.434
Gnomad4 FIN
AF:
0.603
Gnomad4 NFE
AF:
0.571
Gnomad4 OTH
AF:
0.507
Alfa
AF:
0.525
Hom.:
2601
Bravo
AF:
0.501
Asia WGS
AF:
0.463
AC:
1611
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.99
DANN
Benign
0.50

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: rs3848711; hg19: chr20-44446100; API