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GeneBe

1-72358030-C-T

Variant summary

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

The ENST00000665984.1(ENSG00000286863):n.153+74625C>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 0.591 in 151,940 control chromosomes in the GnomAD database, including 27,713 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 ( 27713 hom., cov: 32)

Consequence


ENST00000665984.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.839
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=-0.98).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105378797XR_001737670.2 linkuse as main transcriptn.472+74625C>T intron_variant, non_coding_transcript_variant
LOC105378797XR_001737671.3 linkuse as main transcriptn.472+74625C>T intron_variant, non_coding_transcript_variant
LOC105378797XR_947505.3 linkuse as main transcriptn.472+74625C>T intron_variant, non_coding_transcript_variant
LOC105378797XR_947506.3 linkuse as main transcriptn.472+74625C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000665984.1 linkuse as main transcriptn.153+74625C>T intron_variant, non_coding_transcript_variant
ENST00000653965.1 linkuse as main transcriptn.236+74625C>T intron_variant, non_coding_transcript_variant
ENST00000667836.1 linkuse as main transcriptn.227+74625C>T intron_variant, non_coding_transcript_variant
ENST00000688733.1 linkuse as main transcriptn.56+74625C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.592
AC:
89813
AN:
151822
Hom.:
27705
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.432
Gnomad AMI
AF:
0.555
Gnomad AMR
AF:
0.694
Gnomad ASJ
AF:
0.737
Gnomad EAS
AF:
0.921
Gnomad SAS
AF:
0.663
Gnomad FIN
AF:
0.652
Gnomad MID
AF:
0.722
Gnomad NFE
AF:
0.618
Gnomad OTH
AF:
0.623
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:
0.591
AC:
89839
AN:
151940
Hom.:
27713
Cov.:
32
AF XY:
0.599
AC XY:
44501
AN XY:
74286
show subpopulations
Gnomad4 AFR
AF:
0.431
Gnomad4 AMR
AF:
0.694
Gnomad4 ASJ
AF:
0.737
Gnomad4 EAS
AF:
0.920
Gnomad4 SAS
AF:
0.664
Gnomad4 FIN
AF:
0.652
Gnomad4 NFE
AF:
0.618
Gnomad4 OTH
AF:
0.626
Alfa
AF:
0.627
Hom.:
27542
Bravo
AF:
0.590
Asia WGS
AF:
0.742
AC:
2572
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
Cadd
Benign
0.88
Dann
Benign
0.72

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: rs990871; hg19: chr1-72823713; API