rs7061408

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 0.333 in 111,450 control chromosomes in the GnomAD database, including 5,554 homozygotes. There are 10,824 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 0.33 ( 5554 hom., 10824 hem., cov: 23)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.830
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=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 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:
0.333
AC:
37119
AN:
111400
Hom.:
5554
Cov.:
23
AF XY:
0.321
AC XY:
10793
AN XY:
33634
show subpopulations
Gnomad AFR
AF:
0.585
Gnomad AMI
AF:
0.219
Gnomad AMR
AF:
0.334
Gnomad ASJ
AF:
0.205
Gnomad EAS
AF:
0.101
Gnomad SAS
AF:
0.253
Gnomad FIN
AF:
0.216
Gnomad MID
AF:
0.260
Gnomad NFE
AF:
0.230
Gnomad OTH
AF:
0.288
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.333
AC:
37147
AN:
111450
Hom.:
5554
Cov.:
23
AF XY:
0.321
AC XY:
10824
AN XY:
33694
show subpopulations
Gnomad4 AFR
AF:
0.585
Gnomad4 AMR
AF:
0.334
Gnomad4 ASJ
AF:
0.205
Gnomad4 EAS
AF:
0.101
Gnomad4 SAS
AF:
0.254
Gnomad4 FIN
AF:
0.216
Gnomad4 NFE
AF:
0.230
Gnomad4 OTH
AF:
0.285
Alfa
AF:
0.294
Hom.:
1881
Bravo
AF:
0.355

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
1.8
DANN
Benign
0.29

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: rs7061408; hg19: chrX-82187693; API