rs2739771

Variant summary

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

The ENST00000424333.6(SNHG14):​n.381C>T 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 0.0135 in 499,316 control chromosomes in the GnomAD database, including 125 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 0.025 ( 92 hom., cov: 33)
Exomes 𝑓: 0.0084 ( 33 hom. )

Consequence

SNHG14
ENST00000424333.6 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.481
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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0668 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SNHG14NR_146177.1 linkuse as main transcriptn.13308C>T non_coding_transcript_exon_variant 93/148

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SNHG14ENST00000424333.6 linkuse as main transcriptn.381C>T non_coding_transcript_exon_variant 5/541
SNHG14ENST00000424208.5 linkuse as main transcriptn.1931C>T non_coding_transcript_exon_variant 21/345
SNHG14ENST00000653489.1 linkuse as main transcriptn.295C>T non_coding_transcript_exon_variant 4/59
SNHG14ENST00000656420.1 linkuse as main transcriptn.850C>T non_coding_transcript_exon_variant 7/57

Frequencies

GnomAD3 genomes
AF:
0.0248
AC:
3780
AN:
152180
Hom.:
88
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0684
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0170
Gnomad ASJ
AF:
0.0259
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00228
Gnomad FIN
AF:
0.00744
Gnomad MID
AF:
0.0190
Gnomad NFE
AF:
0.00672
Gnomad OTH
AF:
0.0201
GnomAD4 exome
AF:
0.00842
AC:
2921
AN:
347018
Hom.:
33
Cov.:
0
AF XY:
0.00754
AC XY:
1507
AN XY:
199972
show subpopulations
Gnomad4 AFR exome
AF:
0.0674
Gnomad4 AMR exome
AF:
0.00960
Gnomad4 ASJ exome
AF:
0.0219
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00186
Gnomad4 FIN exome
AF:
0.00726
Gnomad4 NFE exome
AF:
0.00690
Gnomad4 OTH exome
AF:
0.0137
GnomAD4 genome
AF:
0.0250
AC:
3811
AN:
152298
Hom.:
92
Cov.:
33
AF XY:
0.0249
AC XY:
1851
AN XY:
74462
show subpopulations
Gnomad4 AFR
AF:
0.0689
Gnomad4 AMR
AF:
0.0170
Gnomad4 ASJ
AF:
0.0259
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00249
Gnomad4 FIN
AF:
0.00744
Gnomad4 NFE
AF:
0.00673
Gnomad4 OTH
AF:
0.0203
Alfa
AF:
0.0206
Hom.:
15
Bravo
AF:
0.0266
Asia WGS
AF:
0.00751
AC:
26
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
2.6
DANN
Benign
0.27

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: rs2739771; hg19: chr15-25446356; API