1-95568926-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 0.726 in 151,960 control chromosomes in the GnomAD database, including 41,211 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 0.73 ( 41211 hom., cov: 32)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.122
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=-0.81).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.95568926C>T intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC02607ENST00000456933.1 linkuse as main transcriptn.307+30234C>T intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.726
AC:
110299
AN:
151842
Hom.:
41217
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.566
Gnomad AMI
AF:
0.847
Gnomad AMR
AF:
0.734
Gnomad ASJ
AF:
0.784
Gnomad EAS
AF:
0.508
Gnomad SAS
AF:
0.617
Gnomad FIN
AF:
0.804
Gnomad MID
AF:
0.715
Gnomad NFE
AF:
0.829
Gnomad OTH
AF:
0.755
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.726
AC:
110311
AN:
151960
Hom.:
41211
Cov.:
32
AF XY:
0.720
AC XY:
53504
AN XY:
74282
show subpopulations
Gnomad4 AFR
AF:
0.565
Gnomad4 AMR
AF:
0.733
Gnomad4 ASJ
AF:
0.784
Gnomad4 EAS
AF:
0.508
Gnomad4 SAS
AF:
0.618
Gnomad4 FIN
AF:
0.804
Gnomad4 NFE
AF:
0.829
Gnomad4 OTH
AF:
0.748
Alfa
AF:
0.810
Hom.:
90994
Bravo
AF:
0.719
Asia WGS
AF:
0.525
AC:
1827
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
4.1
DANN
Benign
0.54

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: rs6593669; hg19: chr1-96034482; API