rs951095

Variant summary

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

The XR_001749995.2(LOC107984606):​n.296+10910G>A 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 0.384 in 151,906 control chromosomes in the GnomAD database, including 11,588 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 0.38 ( 11588 hom., cov: 31)

Consequence

LOC107984606
XR_001749995.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0530
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 (AMR) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC107984606XR_001749995.2 linkuse as main transcriptn.296+10910G>A intron_variant, non_coding_transcript_variant
LOC107984607XR_007063861.1 linkuse as main transcriptn.87+2814C>T intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.385
AC:
58374
AN:
151788
Hom.:
11591
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.385
Gnomad AMI
AF:
0.393
Gnomad AMR
AF:
0.471
Gnomad ASJ
AF:
0.247
Gnomad EAS
AF:
0.412
Gnomad SAS
AF:
0.419
Gnomad FIN
AF:
0.522
Gnomad MID
AF:
0.320
Gnomad NFE
AF:
0.348
Gnomad OTH
AF:
0.343
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.384
AC:
58393
AN:
151906
Hom.:
11588
Cov.:
31
AF XY:
0.397
AC XY:
29462
AN XY:
74204
show subpopulations
Gnomad4 AFR
AF:
0.385
Gnomad4 AMR
AF:
0.471
Gnomad4 ASJ
AF:
0.247
Gnomad4 EAS
AF:
0.412
Gnomad4 SAS
AF:
0.418
Gnomad4 FIN
AF:
0.522
Gnomad4 NFE
AF:
0.348
Gnomad4 OTH
AF:
0.340
Alfa
AF:
0.347
Hom.:
19759
Bravo
AF:
0.379
Asia WGS
AF:
0.415
AC:
1445
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
2.9
DANN
Benign
0.63

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: rs951095; hg19: chr13-105478644; API