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GeneBe

rs16960351

chr15-47921780-A-G

Variant summary

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

The ENST00000662551.1(ENSG00000259754):n.189-70929A>G 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 0.044 in 152,150 control chromosomes in the GnomAD database, including 400 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 0.044 ( 400 hom., cov: 32)

Consequence


ENST00000662551.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.23
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
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124900354XR_001751516.3 linkuse as main transcriptn.142+37276A>G intron_variant, non_coding_transcript_variant
LOC124900354XR_001751517.2 linkuse as main transcriptn.142+37276A>G intron_variant, non_coding_transcript_variant
LOC124900354XR_001751518.3 linkuse as main transcriptn.82+6418A>G intron_variant, non_coding_transcript_variant
LOC124900354XR_007064618.1 linkuse as main transcriptn.143-27576A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000662551.1 linkuse as main transcriptn.189-70929A>G intron_variant, non_coding_transcript_variant
ENST00000560900.1 linkuse as main transcriptn.195+37276A>G intron_variant, non_coding_transcript_variant 4
ENST00000664705.1 linkuse as main transcriptn.189-70929A>G intron_variant, non_coding_transcript_variant
ENST00000665188.1 linkuse as main transcriptn.69-70929A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0438
AC:
6663
AN:
152032
Hom.:
396
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.118
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0814
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00511
Gnomad SAS
AF:
0.0745
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000559
Gnomad OTH
AF:
0.0435
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0440
AC:
6689
AN:
152150
Hom.:
400
Cov.:
32
AF XY:
0.0443
AC XY:
3295
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.119
Gnomad4 AMR
AF:
0.0819
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00512
Gnomad4 SAS
AF:
0.0735
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000559
Gnomad4 OTH
AF:
0.0430
Alfa
AF:
0.0383
Hom.:
28
Bravo
AF:
0.0553
Asia WGS
AF:
0.0540
AC:
190
AN:
3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
Cadd
Benign
5.1
Dann
Benign
0.45

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: rs16960351; hg19: chr15-48213977; API