7-125933854-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000411856.1(ENSG00000197462):​n.*22T>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 151,878 control chromosomes in the GnomAD database, including 42,172 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 0.74 ( 42171 hom., cov: 32)
Exomes 𝑓: 1.0 ( 1 hom. )

Consequence

ENSG00000197462
ENST00000411856.1 downstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.07
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=-0.98).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.806 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
ENSG00000197462ENST00000411856.1 linkn.*22T>G downstream_gene_variant 3

Frequencies

GnomAD3 genomes
AF:
0.744
AC:
112911
AN:
151758
Hom.:
42146
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.696
Gnomad AMI
AF:
0.679
Gnomad AMR
AF:
0.818
Gnomad ASJ
AF:
0.832
Gnomad EAS
AF:
0.745
Gnomad SAS
AF:
0.789
Gnomad FIN
AF:
0.711
Gnomad MID
AF:
0.788
Gnomad NFE
AF:
0.754
Gnomad OTH
AF:
0.766
GnomAD4 exome
AF:
1.00
AC:
2
AN:
2
Hom.:
1
Cov.:
0
AF XY:
1.00
AC XY:
2
AN XY:
2
show subpopulations
Gnomad4 NFE exome
AF:
1.00
GnomAD4 genome
AF:
0.744
AC:
112980
AN:
151876
Hom.:
42171
Cov.:
32
AF XY:
0.743
AC XY:
55131
AN XY:
74236
show subpopulations
Gnomad4 AFR
AF:
0.696
Gnomad4 AMR
AF:
0.818
Gnomad4 ASJ
AF:
0.832
Gnomad4 EAS
AF:
0.745
Gnomad4 SAS
AF:
0.789
Gnomad4 FIN
AF:
0.711
Gnomad4 NFE
AF:
0.754
Gnomad4 OTH
AF:
0.764
Alfa
AF:
0.756
Hom.:
21835
Bravo
AF:
0.750
Asia WGS
AF:
0.747
AC:
2598
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
0.23
DANN
Benign
0.71

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: rs10256927; hg19: chr7-125573908; API