GeneBe

rs230827

Positions:

Variant summary

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

The NR_104668.1(LOC101928505):​n.101-6262G>C 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 0.344 in 151,896 control chromosomes in the GnomAD database, including 11,779 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 0.34 ( 11779 hom., cov: 32)

Consequence

LOC101928505
NR_104668.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.14
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=-0.69).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC101928505NR_104668.1 linkuse as main transcriptn.101-6262G>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000701975.1 linkuse as main transcriptn.227-6262G>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.344
AC:
52160
AN:
151778
Hom.:
11736
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.645
Gnomad AMI
AF:
0.148
Gnomad AMR
AF:
0.269
Gnomad ASJ
AF:
0.210
Gnomad EAS
AF:
0.311
Gnomad SAS
AF:
0.152
Gnomad FIN
AF:
0.258
Gnomad MID
AF:
0.229
Gnomad NFE
AF:
0.217
Gnomad OTH
AF:
0.335
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.344
AC:
52270
AN:
151896
Hom.:
11779
Cov.:
32
AF XY:
0.340
AC XY:
25283
AN XY:
74256
show subpopulations
Gnomad4 AFR
AF:
0.645
Gnomad4 AMR
AF:
0.269
Gnomad4 ASJ
AF:
0.210
Gnomad4 EAS
AF:
0.311
Gnomad4 SAS
AF:
0.153
Gnomad4 FIN
AF:
0.258
Gnomad4 NFE
AF:
0.217
Gnomad4 OTH
AF:
0.334
Alfa
AF:
0.276
Hom.:
894
Bravo
AF:
0.361
Asia WGS
AF:
0.297
AC:
1032
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.69
CADD
Benign
6.6
DANN
Benign
0.84

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: rs230827; hg19: chr5-56954816; API