rs1040398

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 0.0671 in 111,678 control chromosomes in the GnomAD database, including 460 homozygotes. There are 2,148 hemizygotes in GnomAD. 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 0.067 ( 460 hom., 2148 hem., cov: 24)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.334
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 (SAS) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0670
AC:
7474
AN:
111629
Hom.:
458
Cov.:
24
AF XY:
0.0631
AC XY:
2133
AN XY:
33791
show subpopulations
Gnomad AFR
AF:
0.172
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0813
Gnomad ASJ
AF:
0.0211
Gnomad EAS
AF:
0.147
Gnomad SAS
AF:
0.180
Gnomad FIN
AF:
0.00215
Gnomad MID
AF:
0.00840
Gnomad NFE
AF:
0.00370
Gnomad OTH
AF:
0.0612
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0671
AC:
7496
AN:
111678
Hom.:
460
Cov.:
24
AF XY:
0.0635
AC XY:
2148
AN XY:
33850
show subpopulations
Gnomad4 AFR
AF:
0.172
Gnomad4 AMR
AF:
0.0808
Gnomad4 ASJ
AF:
0.0211
Gnomad4 EAS
AF:
0.148
Gnomad4 SAS
AF:
0.179
Gnomad4 FIN
AF:
0.00215
Gnomad4 NFE
AF:
0.00370
Gnomad4 OTH
AF:
0.0703
Alfa
AF:
0.0169
Hom.:
918
Bravo
AF:
0.0772

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
1.0
DANN
Benign
0.45

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: rs1040398; hg19: chrX-43625431; API