chr10-2307125-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000418295.1(LINC00701):​n.47-816T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0414 in 152,272 control chromosomes in the GnomAD database, including 229 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 0.041 ( 229 hom., cov: 33)

Consequence

LINC00701
ENST00000418295.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.21

Publications

0 publications found
Variant links:
Genes affected
LINC00701 (HGNC:44674): (long intergenic non-protein coding RNA 701)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0791 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LINC00701NR_038884.1 linkn.46-816T>A intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC00701ENST00000418295.1 linkn.47-816T>A intron_variant Intron 1 of 2 1
LINC00701ENST00000721387.1 linkn.57-816T>A intron_variant Intron 1 of 5
LINC00701ENST00000721388.1 linkn.47-816T>A intron_variant Intron 1 of 5

Frequencies

GnomAD3 genomes
AF:
0.0413
AC:
6286
AN:
152154
Hom.:
225
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0739
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.0824
Gnomad ASJ
AF:
0.0176
Gnomad EAS
AF:
0.0850
Gnomad SAS
AF:
0.0172
Gnomad FIN
AF:
0.00612
Gnomad MID
AF:
0.0475
Gnomad NFE
AF:
0.0177
Gnomad OTH
AF:
0.0450
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0414
AC:
6308
AN:
152272
Hom.:
229
Cov.:
33
AF XY:
0.0410
AC XY:
3053
AN XY:
74474
show subpopulations
African (AFR)
AF:
0.0740
AC:
3074
AN:
41546
American (AMR)
AF:
0.0829
AC:
1268
AN:
15302
Ashkenazi Jewish (ASJ)
AF:
0.0176
AC:
61
AN:
3472
East Asian (EAS)
AF:
0.0848
AC:
439
AN:
5176
South Asian (SAS)
AF:
0.0174
AC:
84
AN:
4830
European-Finnish (FIN)
AF:
0.00612
AC:
65
AN:
10620
Middle Eastern (MID)
AF:
0.0476
AC:
14
AN:
294
European-Non Finnish (NFE)
AF:
0.0177
AC:
1205
AN:
68010
Other (OTH)
AF:
0.0460
AC:
97
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
298
596
894
1192
1490
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
70
140
210
280
350
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.00971
Hom.:
2
Bravo
AF:
0.0483
Asia WGS
AF:
0.0680
AC:
235
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
15
DANN
Benign
0.62
PhyloP100
2.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs12265908; hg19: chr10-2349319; API