rs7107217

Variant summary

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

The ENST00000626400.1(ENSG00000281386):​n.129-7917A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 152,066 control chromosomes in the GnomAD database, including 23,069 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 0.55 ( 23069 hom., cov: 33)

Consequence

ENSG00000281386
ENST00000626400.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.649
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=-0.87).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.614 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
ENSG00000281386ENST00000626400.1 linkn.129-7917A>C intron_variant Intron 1 of 1 4

Frequencies

GnomAD3 genomes
AF:
0.547
AC:
83121
AN:
151948
Hom.:
23059
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.549
Gnomad AMI
AF:
0.580
Gnomad AMR
AF:
0.537
Gnomad ASJ
AF:
0.612
Gnomad EAS
AF:
0.347
Gnomad SAS
AF:
0.632
Gnomad FIN
AF:
0.476
Gnomad MID
AF:
0.611
Gnomad NFE
AF:
0.564
Gnomad OTH
AF:
0.561
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.547
AC:
83153
AN:
152066
Hom.:
23069
Cov.:
33
AF XY:
0.544
AC XY:
40431
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.548
Gnomad4 AMR
AF:
0.537
Gnomad4 ASJ
AF:
0.612
Gnomad4 EAS
AF:
0.347
Gnomad4 SAS
AF:
0.633
Gnomad4 FIN
AF:
0.476
Gnomad4 NFE
AF:
0.564
Gnomad4 OTH
AF:
0.555
Alfa
AF:
0.556
Hom.:
23125
Bravo
AF:
0.544

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
6.2
DANN
Benign
0.83

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: rs7107217; hg19: chr11-129473690; API