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GeneBe

rs4775728

chr15-47999368-C-G

Variant summary

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

The ENST00000662551.1(ENSG00000259754):n.251+6597C>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 0.0509 in 152,212 control chromosomes in the GnomAD database, including 530 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 0.051 ( 530 hom., cov: 32)

Consequence


ENST00000662551.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.119
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=-0.83).
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 = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124900354XR_001751516.3 linkuse as main transcriptn.205+6597C>G intron_variant, non_coding_transcript_variant
LOC102724553XR_001751520.2 linkuse as main transcriptn.262+3340G>C intron_variant, non_coding_transcript_variant
LOC124900354XR_001751518.3 linkuse as main transcriptn.145+6597C>G intron_variant, non_coding_transcript_variant
LOC102724553XR_001751521.2 linkuse as main transcriptn.262+3340G>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000662551.1 linkuse as main transcriptn.251+6597C>G intron_variant, non_coding_transcript_variant
ENST00000560900.1 linkuse as main transcriptn.258+6597C>G intron_variant, non_coding_transcript_variant 4
ENST00000664705.1 linkuse as main transcriptn.319+1213C>G intron_variant, non_coding_transcript_variant
ENST00000665188.1 linkuse as main transcriptn.220+1213C>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0507
AC:
7710
AN:
152094
Hom.:
524
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.139
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0877
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00500
Gnomad SAS
AF:
0.0951
Gnomad FIN
AF:
0.000377
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000647
Gnomad OTH
AF:
0.0430
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:
0.0509
AC:
7754
AN:
152212
Hom.:
530
Cov.:
32
AF XY:
0.0509
AC XY:
3787
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.139
Gnomad4 AMR
AF:
0.0882
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00501
Gnomad4 SAS
AF:
0.0941
Gnomad4 FIN
AF:
0.000377
Gnomad4 NFE
AF:
0.000647
Gnomad4 OTH
AF:
0.0425
Alfa
AF:
0.0277
Hom.:
25
Bravo
AF:
0.0623
Asia WGS
AF:
0.0650
AC:
228
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
2.0
Dann
Benign
0.67

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: rs4775728; hg19: chr15-48291565; API