rs10484113

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 0.399 in 151,940 control chromosomes in the GnomAD database, including 13,329 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 0.40 ( 13329 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.359
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=-0.88).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.545 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:
0.399
AC:
60578
AN:
151820
Hom.:
13318
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.224
Gnomad AMI
AF:
0.497
Gnomad AMR
AF:
0.554
Gnomad ASJ
AF:
0.543
Gnomad EAS
AF:
0.293
Gnomad SAS
AF:
0.465
Gnomad FIN
AF:
0.354
Gnomad MID
AF:
0.472
Gnomad NFE
AF:
0.471
Gnomad OTH
AF:
0.435
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.399
AC:
60607
AN:
151940
Hom.:
13329
Cov.:
31
AF XY:
0.399
AC XY:
29618
AN XY:
74260
show subpopulations
Gnomad4 AFR
AF:
0.224
Gnomad4 AMR
AF:
0.555
Gnomad4 ASJ
AF:
0.543
Gnomad4 EAS
AF:
0.293
Gnomad4 SAS
AF:
0.466
Gnomad4 FIN
AF:
0.354
Gnomad4 NFE
AF:
0.471
Gnomad4 OTH
AF:
0.429
Alfa
AF:
0.468
Hom.:
18397
Bravo
AF:
0.407
Asia WGS
AF:
0.345
AC:
1191
AN:
3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
2.8
DANN
Benign
0.74

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: rs10484113; hg19: chr14-85477753; API