chr10-6077003-C-T

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 0.442 in 151,922 control chromosomes in the GnomAD database, including 16,846 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 0.44 ( 16846 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.832
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=-0.98).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 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:
0.443
AC:
67176
AN:
151804
Hom.:
16833
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.215
Gnomad AMI
AF:
0.524
Gnomad AMR
AF:
0.453
Gnomad ASJ
AF:
0.578
Gnomad EAS
AF:
0.289
Gnomad SAS
AF:
0.522
Gnomad FIN
AF:
0.522
Gnomad MID
AF:
0.576
Gnomad NFE
AF:
0.562
Gnomad OTH
AF:
0.488
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.442
AC:
67201
AN:
151922
Hom.:
16846
Cov.:
30
AF XY:
0.440
AC XY:
32632
AN XY:
74224
show subpopulations
Gnomad4 AFR
AF:
0.215
Gnomad4 AMR
AF:
0.452
Gnomad4 ASJ
AF:
0.578
Gnomad4 EAS
AF:
0.288
Gnomad4 SAS
AF:
0.524
Gnomad4 FIN
AF:
0.522
Gnomad4 NFE
AF:
0.562
Gnomad4 OTH
AF:
0.492
Alfa
AF:
0.545
Hom.:
46619
Bravo
AF:
0.423
Asia WGS
AF:
0.409
AC:
1426
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.39
DANN
Benign
0.48

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: rs4749955; hg19: chr10-6118966; API