chr6-163401264-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 0.356 in 152,140 control chromosomes in the GnomAD database, including 11,301 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 0.36 ( 11301 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.139
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 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:
0.356
AC:
54134
AN:
152020
Hom.:
11296
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.151
Gnomad AMI
AF:
0.402
Gnomad AMR
AF:
0.330
Gnomad ASJ
AF:
0.405
Gnomad EAS
AF:
0.714
Gnomad SAS
AF:
0.485
Gnomad FIN
AF:
0.513
Gnomad MID
AF:
0.304
Gnomad NFE
AF:
0.423
Gnomad OTH
AF:
0.365
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.356
AC:
54152
AN:
152140
Hom.:
11301
Cov.:
33
AF XY:
0.363
AC XY:
27029
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.150
Gnomad4 AMR
AF:
0.330
Gnomad4 ASJ
AF:
0.405
Gnomad4 EAS
AF:
0.714
Gnomad4 SAS
AF:
0.484
Gnomad4 FIN
AF:
0.513
Gnomad4 NFE
AF:
0.423
Gnomad4 OTH
AF:
0.367
Alfa
AF:
0.378
Hom.:
4964
Bravo
AF:
0.331
Asia WGS
AF:
0.574
AC:
1994
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.77
DANN
Benign
0.61

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: rs4263561; hg19: chr6-163822296; COSMIC: COSV69432263; API