rs10805321

Variant summary

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

The NR_121681.1(LINC01182):​n.350-16601C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,006 control chromosomes in the GnomAD database, including 2,225 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 0.17 ( 2225 hom., cov: 32)

Consequence

LINC01182
NR_121681.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.843
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 (SAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC01182NR_121681.1 linkuse as main transcriptn.350-16601C>A intron_variant
LOC107986182XR_001741382.2 linkuse as main transcriptn.3015-18795C>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC01182ENST00000503532.1 linkuse as main transcriptn.231-47240C>A intron_variant 4
LINC01182ENST00000510907.5 linkuse as main transcriptn.350-16601C>A intron_variant 2
LINC01182ENST00000669061.1 linkuse as main transcriptn.713+74290C>A intron_variant

Frequencies

GnomAD3 genomes
AF:
0.169
AC:
25602
AN:
151886
Hom.:
2215
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.143
Gnomad AMI
AF:
0.273
Gnomad AMR
AF:
0.202
Gnomad ASJ
AF:
0.202
Gnomad EAS
AF:
0.183
Gnomad SAS
AF:
0.267
Gnomad FIN
AF:
0.172
Gnomad MID
AF:
0.266
Gnomad NFE
AF:
0.163
Gnomad OTH
AF:
0.201
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.169
AC:
25632
AN:
152006
Hom.:
2225
Cov.:
32
AF XY:
0.173
AC XY:
12882
AN XY:
74284
show subpopulations
Gnomad4 AFR
AF:
0.143
Gnomad4 AMR
AF:
0.203
Gnomad4 ASJ
AF:
0.202
Gnomad4 EAS
AF:
0.183
Gnomad4 SAS
AF:
0.268
Gnomad4 FIN
AF:
0.172
Gnomad4 NFE
AF:
0.163
Gnomad4 OTH
AF:
0.200
Alfa
AF:
0.170
Hom.:
3780
Bravo
AF:
0.167
Asia WGS
AF:
0.242
AC:
841
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.69
CADD
Benign
2.5
DANN
Benign
0.91

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: rs10805321; hg19: chr4-13914373; API