10-37679350-A-G

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PVS1_ModerateBA1

The XR_930828.2(LOC105376498):​n.479+2T>C variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 152,092 control chromosomes in the GnomAD database, including 17,193 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 0.47 ( 17193 hom., cov: 33)

Consequence

LOC105376498
XR_930828.2 splice_donor, intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.67
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

PVS1
Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105376498XR_930828.2 linkn.479+2T>C splice_donor_variant, intron_variant Intron 2 of 3
LOC105376498XR_930829.2 linkn.414+545T>C intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.470
AC:
71496
AN:
151972
Hom.:
17155
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.457
Gnomad AMI
AF:
0.475
Gnomad AMR
AF:
0.527
Gnomad ASJ
AF:
0.459
Gnomad EAS
AF:
0.548
Gnomad SAS
AF:
0.312
Gnomad FIN
AF:
0.320
Gnomad MID
AF:
0.547
Gnomad NFE
AF:
0.494
Gnomad OTH
AF:
0.497
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.471
AC:
71586
AN:
152092
Hom.:
17193
Cov.:
33
AF XY:
0.464
AC XY:
34466
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.458
Gnomad4 AMR
AF:
0.527
Gnomad4 ASJ
AF:
0.459
Gnomad4 EAS
AF:
0.549
Gnomad4 SAS
AF:
0.310
Gnomad4 FIN
AF:
0.320
Gnomad4 NFE
AF:
0.494
Gnomad4 OTH
AF:
0.495
Alfa
AF:
0.488
Hom.:
9672
Bravo
AF:
0.492
Asia WGS
AF:
0.473
AC:
1645
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.81
DANN
Benign
0.29

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: rs289647; hg19: chr10-37968278; API