GeneBe

6-31368473-A-G

Position:

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 152,186 control chromosomes in the GnomAD database, including 8,066 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 ( 8066 hom., cov: 33)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.660
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=-0.94).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.31368473A>G intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000285647ENST00000649421.1 linkuse as main transcriptn.274+1143A>G intron_variant

Frequencies

GnomAD3 genomes
AF:
0.315
AC:
47890
AN:
152068
Hom.:
8063
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.258
Gnomad AMI
AF:
0.375
Gnomad AMR
AF:
0.265
Gnomad ASJ
AF:
0.177
Gnomad EAS
AF:
0.214
Gnomad SAS
AF:
0.225
Gnomad FIN
AF:
0.272
Gnomad MID
AF:
0.294
Gnomad NFE
AF:
0.388
Gnomad OTH
AF:
0.316
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.315
AC:
47911
AN:
152186
Hom.:
8066
Cov.:
33
AF XY:
0.304
AC XY:
22597
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.258
Gnomad4 AMR
AF:
0.265
Gnomad4 ASJ
AF:
0.177
Gnomad4 EAS
AF:
0.213
Gnomad4 SAS
AF:
0.225
Gnomad4 FIN
AF:
0.272
Gnomad4 NFE
AF:
0.388
Gnomad4 OTH
AF:
0.313
Alfa
AF:
0.355
Hom.:
7508
Bravo
AF:
0.314
Asia WGS
AF:
0.231
AC:
803
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
6.2
DANN
Benign
0.43

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: rs2523535; hg19: chr6-31336250; API