chr1-83757355-A-G

Variant summary

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

The NR_119375.1(LINC01725):​n.179-7056T>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 0.136 in 152,058 control chromosomes in the GnomAD database, including 1,574 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 0.14 ( 1574 hom., cov: 32)

Consequence

LINC01725
NR_119375.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.949
Variant links:
Genes affected
LINC01725 (HGNC:52513): (long intergenic non-protein coding RNA 1725)

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=-0.81).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC01725NR_119375.1 linkuse as main transcriptn.179-7056T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC01725ENST00000417975.1 linkuse as main transcriptn.179-7056T>C intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.136
AC:
20654
AN:
151940
Hom.:
1574
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0834
Gnomad AMI
AF:
0.140
Gnomad AMR
AF:
0.107
Gnomad ASJ
AF:
0.127
Gnomad EAS
AF:
0.118
Gnomad SAS
AF:
0.109
Gnomad FIN
AF:
0.176
Gnomad MID
AF:
0.0823
Gnomad NFE
AF:
0.172
Gnomad OTH
AF:
0.133
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.136
AC:
20655
AN:
152058
Hom.:
1574
Cov.:
32
AF XY:
0.134
AC XY:
9984
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.0833
Gnomad4 AMR
AF:
0.107
Gnomad4 ASJ
AF:
0.127
Gnomad4 EAS
AF:
0.118
Gnomad4 SAS
AF:
0.109
Gnomad4 FIN
AF:
0.176
Gnomad4 NFE
AF:
0.172
Gnomad4 OTH
AF:
0.131
Alfa
AF:
0.154
Hom.:
1135
Bravo
AF:
0.128
Asia WGS
AF:
0.101
AC:
351
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
5.4
DANN
Benign
0.61

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: rs6663404; hg19: chr1-84223038; API