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GeneBe

rs2934177

Positions:

Variant summary

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

The ENST00000662551.1(ENSG00000259754):​n.189-71359C>T 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 0.975 in 152,226 control chromosomes in the GnomAD database, including 72,555 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 0.97 ( 72555 hom., cov: 33)

Consequence


ENST00000662551.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.66
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=-1.0).
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 = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124900354XR_001751516.3 linkuse as main transcriptn.142+36846C>T intron_variant, non_coding_transcript_variant
LOC124900354XR_001751517.2 linkuse as main transcriptn.142+36846C>T intron_variant, non_coding_transcript_variant
LOC124900354XR_001751518.3 linkuse as main transcriptn.82+5988C>T intron_variant, non_coding_transcript_variant
LOC124900354XR_007064618.1 linkuse as main transcriptn.143-28006C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000662551.1 linkuse as main transcriptn.189-71359C>T intron_variant, non_coding_transcript_variant
ENST00000560900.1 linkuse as main transcriptn.195+36846C>T intron_variant, non_coding_transcript_variant 4
ENST00000664705.1 linkuse as main transcriptn.189-71359C>T intron_variant, non_coding_transcript_variant
ENST00000665188.1 linkuse as main transcriptn.69-71359C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.975
AC:
148259
AN:
152102
Hom.:
72496
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.987
Gnomad AMI
AF:
0.988
Gnomad AMR
AF:
0.961
Gnomad ASJ
AF:
0.979
Gnomad EAS
AF:
0.725
Gnomad SAS
AF:
0.979
Gnomad FIN
AF:
0.986
Gnomad MID
AF:
0.987
Gnomad NFE
AF:
0.986
Gnomad OTH
AF:
0.974
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:
0.975
AC:
148380
AN:
152226
Hom.:
72555
Cov.:
33
AF XY:
0.973
AC XY:
72421
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.987
Gnomad4 AMR
AF:
0.961
Gnomad4 ASJ
AF:
0.979
Gnomad4 EAS
AF:
0.725
Gnomad4 SAS
AF:
0.979
Gnomad4 FIN
AF:
0.986
Gnomad4 NFE
AF:
0.986
Gnomad4 OTH
AF:
0.974
Alfa
AF:
0.984
Hom.:
9296
Bravo
AF:
0.972
Asia WGS
AF:
0.892
AC:
3092
AN:
3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.040
DANN
Benign
0.68

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: rs2934177; hg19: chr15-48213547; API