chr6-31605150-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 0.0593 in 151,008 control chromosomes in the GnomAD database, including 490 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 0.059 ( 490 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.416
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=-0.66).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 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:
0.0594
AC:
8963
AN:
150894
Hom.:
490
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0123
Gnomad AMI
AF:
0.170
Gnomad AMR
AF:
0.0457
Gnomad ASJ
AF:
0.120
Gnomad EAS
AF:
0.266
Gnomad SAS
AF:
0.192
Gnomad FIN
AF:
0.0370
Gnomad MID
AF:
0.0605
Gnomad NFE
AF:
0.0648
Gnomad OTH
AF:
0.0564
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0593
AC:
8960
AN:
151008
Hom.:
490
Cov.:
30
AF XY:
0.0622
AC XY:
4587
AN XY:
73708
show subpopulations
Gnomad4 AFR
AF:
0.0123
Gnomad4 AMR
AF:
0.0458
Gnomad4 ASJ
AF:
0.120
Gnomad4 EAS
AF:
0.266
Gnomad4 SAS
AF:
0.191
Gnomad4 FIN
AF:
0.0370
Gnomad4 NFE
AF:
0.0647
Gnomad4 OTH
AF:
0.0577
Alfa
AF:
0.0670
Hom.:
476
Bravo
AF:
0.0544
Asia WGS
AF:
0.155
AC:
536
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
CADD
Benign
15
DANN
Benign
0.91

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: rs9378200; hg19: chr6-31572927; API