chr4-10164155-G-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 0.315 in 152,100 control chromosomes in the GnomAD database, including 7,598 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 0.31 ( 7598 hom., cov: 32)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.153
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.10164155G>T intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.315
AC:
47856
AN:
151982
Hom.:
7599
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.345
Gnomad AMI
AF:
0.243
Gnomad AMR
AF:
0.272
Gnomad ASJ
AF:
0.257
Gnomad EAS
AF:
0.229
Gnomad SAS
AF:
0.381
Gnomad FIN
AF:
0.315
Gnomad MID
AF:
0.245
Gnomad NFE
AF:
0.312
Gnomad OTH
AF:
0.307
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.315
AC:
47882
AN:
152100
Hom.:
7598
Cov.:
32
AF XY:
0.315
AC XY:
23416
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.345
Gnomad4 AMR
AF:
0.272
Gnomad4 ASJ
AF:
0.257
Gnomad4 EAS
AF:
0.228
Gnomad4 SAS
AF:
0.380
Gnomad4 FIN
AF:
0.315
Gnomad4 NFE
AF:
0.313
Gnomad4 OTH
AF:
0.302
Alfa
AF:
0.305
Hom.:
14900
Bravo
AF:
0.309
Asia WGS
AF:
0.316
AC:
1097
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.58
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: rs16894270; hg19: chr4-10165779; API