rs6109595

Variant summary

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

The NR_109868.1(LINC01722):​n.2455+12186T>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 0.116 in 152,124 control chromosomes in the GnomAD database, including 1,192 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 0.12 ( 1192 hom., cov: 32)

Consequence

LINC01722
NR_109868.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.223
Variant links:
Genes affected
LINC01722 (HGNC:52510): (long intergenic non-protein coding RNA 1722)

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=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LINC01722NR_109868.1 linkuse as main transcriptn.2455+12186T>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LINC01722ENST00000456265.1 linkuse as main transcriptn.2455+12186T>G intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.116
AC:
17597
AN:
152006
Hom.:
1190
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.186
Gnomad AMI
AF:
0.121
Gnomad AMR
AF:
0.0928
Gnomad ASJ
AF:
0.134
Gnomad EAS
AF:
0.0509
Gnomad SAS
AF:
0.0779
Gnomad FIN
AF:
0.0440
Gnomad MID
AF:
0.193
Gnomad NFE
AF:
0.0960
Gnomad OTH
AF:
0.112
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.116
AC:
17599
AN:
152124
Hom.:
1192
Cov.:
32
AF XY:
0.113
AC XY:
8380
AN XY:
74378
show subpopulations
Gnomad4 AFR
AF:
0.185
Gnomad4 AMR
AF:
0.0926
Gnomad4 ASJ
AF:
0.134
Gnomad4 EAS
AF:
0.0508
Gnomad4 SAS
AF:
0.0769
Gnomad4 FIN
AF:
0.0440
Gnomad4 NFE
AF:
0.0960
Gnomad4 OTH
AF:
0.113
Alfa
AF:
0.0997
Hom.:
399
Bravo
AF:
0.123
Asia WGS
AF:
0.0810
AC:
284
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
12
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: rs6109595; hg19: chr20-12861103; API