rs959931

Variant summary

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

The ENST00000522627.1(LINC01847):​n.3691+23166G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,038 control chromosomes in the GnomAD database, including 5,174 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 0.25 ( 5174 hom., cov: 32)

Consequence

LINC01847
ENST00000522627.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0440
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=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC01847NR_109891.1 linkuse as main transcriptn.3691+23166G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC01847ENST00000522627.1 linkuse as main transcriptn.3691+23166G>A intron_variant 1
LINC01847ENST00000641163.1 linkuse as main transcriptn.252+24152G>A intron_variant

Frequencies

GnomAD3 genomes
AF:
0.248
AC:
37690
AN:
151920
Hom.:
5162
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.380
Gnomad AMI
AF:
0.202
Gnomad AMR
AF:
0.160
Gnomad ASJ
AF:
0.167
Gnomad EAS
AF:
0.158
Gnomad SAS
AF:
0.207
Gnomad FIN
AF:
0.252
Gnomad MID
AF:
0.193
Gnomad NFE
AF:
0.203
Gnomad OTH
AF:
0.223
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.248
AC:
37739
AN:
152038
Hom.:
5174
Cov.:
32
AF XY:
0.251
AC XY:
18621
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.380
Gnomad4 AMR
AF:
0.160
Gnomad4 ASJ
AF:
0.167
Gnomad4 EAS
AF:
0.158
Gnomad4 SAS
AF:
0.206
Gnomad4 FIN
AF:
0.252
Gnomad4 NFE
AF:
0.203
Gnomad4 OTH
AF:
0.228
Alfa
AF:
0.208
Hom.:
5480
Bravo
AF:
0.246
Asia WGS
AF:
0.194
AC:
673
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
1.5
DANN
Benign
0.67

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: rs959931; hg19: chr5-159270713; API