chr10-43912449-T-G

Variant summary

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

The ENST00000446107.2(LINC00841):​n.60T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 152,212 control chromosomes in the GnomAD database, including 26,639 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 0.59 ( 26586 hom., cov: 31)
Exomes 𝑓: 0.64 ( 53 hom. )

Consequence

LINC00841
ENST00000446107.2 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.48

Publications

3 publications found
Variant links:
Genes affected
LINC00841 (HGNC:27430): (long intergenic non-protein coding RNA 841)
LINC02659 (HGNC:54145): (long intergenic non-protein coding RNA 2659)

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=-1.03).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LINC00841NR_136148.1 linkn.48T>G non_coding_transcript_exon_variant Exon 1 of 2
LINC00841NR_033846.2 linkn.191+2790T>G intron_variant Intron 2 of 7
LINC00841NR_136147.1 linkn.191+2790T>G intron_variant Intron 2 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC00841ENST00000446107.2 linkn.60T>G non_coding_transcript_exon_variant Exon 1 of 2 2
LINC00841ENST00000826345.1 linkn.40T>G non_coding_transcript_exon_variant Exon 1 of 3
LINC00841ENST00000826346.1 linkn.38T>G non_coding_transcript_exon_variant Exon 1 of 5

Frequencies

GnomAD3 genomes
AF:
0.590
AC:
89623
AN:
151834
Hom.:
26569
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.532
Gnomad AMI
AF:
0.573
Gnomad AMR
AF:
0.544
Gnomad ASJ
AF:
0.645
Gnomad EAS
AF:
0.611
Gnomad SAS
AF:
0.693
Gnomad FIN
AF:
0.683
Gnomad MID
AF:
0.693
Gnomad NFE
AF:
0.609
Gnomad OTH
AF:
0.597
GnomAD4 exome
AF:
0.641
AC:
168
AN:
262
Hom.:
53
Cov.:
0
AF XY:
0.644
AC XY:
112
AN XY:
174
show subpopulations
African (AFR)
AF:
0.500
AC:
3
AN:
6
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
0.500
AC:
2
AN:
4
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.610
AC:
50
AN:
82
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.665
AC:
105
AN:
158
Other (OTH)
AF:
0.667
AC:
8
AN:
12
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.510
Heterozygous variant carriers
0
3
6
8
11
14
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.590
AC:
89667
AN:
151950
Hom.:
26586
Cov.:
31
AF XY:
0.595
AC XY:
44192
AN XY:
74250
show subpopulations
African (AFR)
AF:
0.532
AC:
22026
AN:
41410
American (AMR)
AF:
0.543
AC:
8300
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.645
AC:
2240
AN:
3472
East Asian (EAS)
AF:
0.612
AC:
3148
AN:
5148
South Asian (SAS)
AF:
0.692
AC:
3334
AN:
4816
European-Finnish (FIN)
AF:
0.683
AC:
7222
AN:
10570
Middle Eastern (MID)
AF:
0.694
AC:
204
AN:
294
European-Non Finnish (NFE)
AF:
0.609
AC:
41403
AN:
67946
Other (OTH)
AF:
0.601
AC:
1267
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
1920
3840
5761
7681
9601
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
766
1532
2298
3064
3830
<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:
0.596
Hom.:
3373
Bravo
AF:
0.569
Asia WGS
AF:
0.651
AC:
2264
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.28
DANN
Benign
0.47
PhyloP100
-2.5

Splicing

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

Publications

Other links and lift over

dbSNP: rs2274241; hg19: chr10-44407897; API