rs6505172

Variant summary

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

The XR_934656.2(LOC105371721):​n.86-779A>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 0.103 in 152,094 control chromosomes in the GnomAD database, including 1,489 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 0.10 ( 1489 hom., cov: 31)

Consequence

LOC105371721
XR_934656.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.326
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=-0.79).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105371721XR_934656.2 linkuse as main transcriptn.86-779A>G intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.103
AC:
15689
AN:
151976
Hom.:
1485
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.247
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0588
Gnomad ASJ
AF:
0.0677
Gnomad EAS
AF:
0.0452
Gnomad SAS
AF:
0.0961
Gnomad FIN
AF:
0.0411
Gnomad MID
AF:
0.0854
Gnomad NFE
AF:
0.0439
Gnomad OTH
AF:
0.0958
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.103
AC:
15711
AN:
152094
Hom.:
1489
Cov.:
31
AF XY:
0.102
AC XY:
7621
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.247
Gnomad4 AMR
AF:
0.0586
Gnomad4 ASJ
AF:
0.0677
Gnomad4 EAS
AF:
0.0443
Gnomad4 SAS
AF:
0.0956
Gnomad4 FIN
AF:
0.0411
Gnomad4 NFE
AF:
0.0439
Gnomad4 OTH
AF:
0.0948
Alfa
AF:
0.0790
Hom.:
106
Bravo
AF:
0.110
Asia WGS
AF:
0.0800
AC:
277
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
8.0
DANN
Benign
0.76

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: rs6505172; hg19: chr17-28638844; API