rs7276141

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 0.0854 in 152,142 control chromosomes in the GnomAD database, including 1,305 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 0.085 ( 1305 hom., cov: 32)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0830
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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.28809450G>C intergenic_region
N6AMT1XR_007067787.1 linkuse as main transcriptn.936+12455C>G intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.0852
AC:
12959
AN:
152024
Hom.:
1301
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.234
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0938
Gnomad ASJ
AF:
0.0462
Gnomad EAS
AF:
0.136
Gnomad SAS
AF:
0.0414
Gnomad FIN
AF:
0.0298
Gnomad MID
AF:
0.0285
Gnomad NFE
AF:
0.00512
Gnomad OTH
AF:
0.0593
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0854
AC:
12986
AN:
152142
Hom.:
1305
Cov.:
32
AF XY:
0.0867
AC XY:
6447
AN XY:
74398
show subpopulations
Gnomad4 AFR
AF:
0.233
Gnomad4 AMR
AF:
0.0940
Gnomad4 ASJ
AF:
0.0462
Gnomad4 EAS
AF:
0.136
Gnomad4 SAS
AF:
0.0408
Gnomad4 FIN
AF:
0.0298
Gnomad4 NFE
AF:
0.00512
Gnomad4 OTH
AF:
0.0611
Alfa
AF:
0.00723
Hom.:
5
Bravo
AF:
0.0979
Asia WGS
AF:
0.0990
AC:
343
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.24
DANN
Benign
0.39

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: rs7276141; hg19: chr21-30181773; API