6-137797778-T-C

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 0.867 in 152,182 control chromosomes in the GnomAD database, including 57,243 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 0.87 ( 57243 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.84
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 (SAS) allele frequency at 95% confidence interval = 0.864 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:
0.867
AC:
131838
AN:
152064
Hom.:
57221
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.871
Gnomad AMI
AF:
0.830
Gnomad AMR
AF:
0.849
Gnomad ASJ
AF:
0.836
Gnomad EAS
AF:
0.849
Gnomad SAS
AF:
0.883
Gnomad FIN
AF:
0.873
Gnomad MID
AF:
0.839
Gnomad NFE
AF:
0.870
Gnomad OTH
AF:
0.863
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.867
AC:
131911
AN:
152182
Hom.:
57243
Cov.:
32
AF XY:
0.866
AC XY:
64407
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.870
Gnomad4 AMR
AF:
0.849
Gnomad4 ASJ
AF:
0.836
Gnomad4 EAS
AF:
0.849
Gnomad4 SAS
AF:
0.882
Gnomad4 FIN
AF:
0.873
Gnomad4 NFE
AF:
0.870
Gnomad4 OTH
AF:
0.858
Alfa
AF:
0.868
Hom.:
14350
Bravo
AF:
0.864
Asia WGS
AF:
0.833
AC:
2900
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.49
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: rs631609; hg19: chr6-138118915; API