rs1371624

Variant summary

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

The ENST00000424655.1(LINC01934):​n.105-7786A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,902 control chromosomes in the GnomAD database, including 10,150 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 0.36 ( 10150 hom., cov: 32)

Consequence

LINC01934
ENST00000424655.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00
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=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC01934NR_130784.1 linkuse as main transcriptn.359-29427A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC01934ENST00000424170.5 linkuse as main transcriptn.582-6412A>G intron_variant 4
LINC01934ENST00000424655.1 linkuse as main transcriptn.105-7786A>G intron_variant 3
LINC01934ENST00000428474.5 linkuse as main transcriptn.151-20948A>G intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.361
AC:
54816
AN:
151784
Hom.:
10148
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.289
Gnomad AMI
AF:
0.457
Gnomad AMR
AF:
0.320
Gnomad ASJ
AF:
0.386
Gnomad EAS
AF:
0.422
Gnomad SAS
AF:
0.369
Gnomad FIN
AF:
0.353
Gnomad MID
AF:
0.332
Gnomad NFE
AF:
0.408
Gnomad OTH
AF:
0.361
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.361
AC:
54833
AN:
151902
Hom.:
10150
Cov.:
32
AF XY:
0.357
AC XY:
26474
AN XY:
74240
show subpopulations
Gnomad4 AFR
AF:
0.289
Gnomad4 AMR
AF:
0.319
Gnomad4 ASJ
AF:
0.386
Gnomad4 EAS
AF:
0.423
Gnomad4 SAS
AF:
0.369
Gnomad4 FIN
AF:
0.353
Gnomad4 NFE
AF:
0.408
Gnomad4 OTH
AF:
0.358
Alfa
AF:
0.371
Hom.:
1333
Bravo
AF:
0.354
Asia WGS
AF:
0.339
AC:
1176
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.7
DANN
Benign
0.70

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: rs1371624; hg19: chr2-182197987; API