chr6-117450114-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The ENST00000467125.1(ENSG00000282218):​c.547+116740T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0241 in 152,368 control chromosomes in the GnomAD database, including 64 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 0.024 ( 64 hom., cov: 32)

Consequence

ENSG00000282218
ENST00000467125.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0750
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=-0.86).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0241 (3679/152368) while in subpopulation NFE AF= 0.0369 (2512/68040). AF 95% confidence interval is 0.0357. There are 64 homozygotes in gnomad4. There are 1715 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 64 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.117450114A>T intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000282218ENST00000467125.1 linkuse as main transcriptc.547+116740T>A intron_variant 2 ENSP00000487717.1 A0A0J9YVX5

Frequencies

GnomAD3 genomes
AF:
0.0242
AC:
3681
AN:
152250
Hom.:
64
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00644
Gnomad AMI
AF:
0.0888
Gnomad AMR
AF:
0.0144
Gnomad ASJ
AF:
0.0193
Gnomad EAS
AF:
0.0244
Gnomad SAS
AF:
0.0124
Gnomad FIN
AF:
0.0276
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.0369
Gnomad OTH
AF:
0.0211
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0241
AC:
3679
AN:
152368
Hom.:
64
Cov.:
32
AF XY:
0.0230
AC XY:
1715
AN XY:
74514
show subpopulations
Gnomad4 AFR
AF:
0.00642
Gnomad4 AMR
AF:
0.0144
Gnomad4 ASJ
AF:
0.0193
Gnomad4 EAS
AF:
0.0245
Gnomad4 SAS
AF:
0.0120
Gnomad4 FIN
AF:
0.0276
Gnomad4 NFE
AF:
0.0369
Gnomad4 OTH
AF:
0.0213
Alfa
AF:
0.0285
Hom.:
5
Bravo
AF:
0.0226
Asia WGS
AF:
0.0160
AC:
57
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
1.3
DANN
Benign
0.58

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs17635492; hg19: chr6-117771277; API