rs13211073

Variant summary

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

The XR_007059588.1(LOC105375070):​n.192+3348C>T 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 0.252 in 152,202 control chromosomes in the GnomAD database, including 5,075 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 0.25 ( 5075 hom., cov: 33)

Consequence

LOC105375070
XR_007059588.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.36
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=-1.05).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC105375070XR_007059588.1 linkuse as main transcriptn.192+3348C>T intron_variant, non_coding_transcript_variant
POLR1CNM_001318876.2 linkuse as main transcriptc.945+271427C>T intron_variant NP_001305805.1
LOC105375070XR_007059589.1 linkuse as main transcriptn.192+3348C>T intron_variant, non_coding_transcript_variant
LOC105375070XR_926833.3 linkuse as main transcriptn.192+3348C>T intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.252
AC:
38344
AN:
152084
Hom.:
5071
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.182
Gnomad AMI
AF:
0.173
Gnomad AMR
AF:
0.300
Gnomad ASJ
AF:
0.243
Gnomad EAS
AF:
0.147
Gnomad SAS
AF:
0.126
Gnomad FIN
AF:
0.276
Gnomad MID
AF:
0.158
Gnomad NFE
AF:
0.299
Gnomad OTH
AF:
0.253
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.252
AC:
38371
AN:
152202
Hom.:
5075
Cov.:
33
AF XY:
0.249
AC XY:
18556
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.182
Gnomad4 AMR
AF:
0.299
Gnomad4 ASJ
AF:
0.243
Gnomad4 EAS
AF:
0.148
Gnomad4 SAS
AF:
0.126
Gnomad4 FIN
AF:
0.276
Gnomad4 NFE
AF:
0.299
Gnomad4 OTH
AF:
0.251
Alfa
AF:
0.288
Hom.:
8797
Bravo
AF:
0.252
Asia WGS
AF:
0.148
AC:
513
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
0.036
DANN
Benign
0.16

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: rs13211073; hg19: chr6-43768435; API