rs7240405

Variant summary

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

The XR_007066363.1(LOC105372112):​n.178+19851A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.858 in 152,238 control chromosomes in the GnomAD database, including 56,108 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 0.86 ( 56108 hom., cov: 33)

Consequence

LOC105372112
XR_007066363.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.797
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=-0.99).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105372112XR_007066363.1 linkuse as main transcriptn.178+19851A>G intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.858
AC:
130498
AN:
152120
Hom.:
56062
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.883
Gnomad AMI
AF:
0.860
Gnomad AMR
AF:
0.898
Gnomad ASJ
AF:
0.897
Gnomad EAS
AF:
0.872
Gnomad SAS
AF:
0.872
Gnomad FIN
AF:
0.839
Gnomad MID
AF:
0.880
Gnomad NFE
AF:
0.832
Gnomad OTH
AF:
0.865
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.858
AC:
130602
AN:
152238
Hom.:
56108
Cov.:
33
AF XY:
0.861
AC XY:
64082
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.883
Gnomad4 AMR
AF:
0.899
Gnomad4 ASJ
AF:
0.897
Gnomad4 EAS
AF:
0.872
Gnomad4 SAS
AF:
0.873
Gnomad4 FIN
AF:
0.839
Gnomad4 NFE
AF:
0.832
Gnomad4 OTH
AF:
0.867
Alfa
AF:
0.846
Hom.:
66442
Bravo
AF:
0.864
Asia WGS
AF:
0.886
AC:
3081
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.74
DANN
Benign
0.17

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: rs7240405; hg19: chr18-47159090; API