X-137977928-C-T

Variant summary

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

The ENST00000636095.1(ENSG00000283692):​n.362-2362C>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 0.0635 in 111,059 control chromosomes in the GnomAD database, including 386 homozygotes. There are 2,031 hemizygotes in GnomAD. 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 0.064 ( 386 hom., 2031 hem., cov: 22)

Consequence


ENST00000636095.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.240
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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000636095.1 linkuse as main transcriptn.362-2362C>T intron_variant, non_coding_transcript_variant 5
ENST00000637564.1 linkuse as main transcriptn.592-2362C>T intron_variant, non_coding_transcript_variant 5
ENST00000637685.1 linkuse as main transcriptn.315-2362C>T intron_variant, non_coding_transcript_variant 5
ENST00000668975.1 linkuse as main transcriptn.262-2362C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0635
AC:
7050
AN:
111007
Hom.:
386
Cov.:
22
AF XY:
0.0610
AC XY:
2030
AN XY:
33281
show subpopulations
Gnomad AFR
AF:
0.130
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0797
Gnomad ASJ
AF:
0.0700
Gnomad EAS
AF:
0.338
Gnomad SAS
AF:
0.0413
Gnomad FIN
AF:
0.0135
Gnomad MID
AF:
0.0254
Gnomad NFE
AF:
0.0115
Gnomad OTH
AF:
0.0628
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0635
AC:
7056
AN:
111059
Hom.:
386
Cov.:
22
AF XY:
0.0609
AC XY:
2031
AN XY:
33343
show subpopulations
Gnomad4 AFR
AF:
0.130
Gnomad4 AMR
AF:
0.0799
Gnomad4 ASJ
AF:
0.0700
Gnomad4 EAS
AF:
0.338
Gnomad4 SAS
AF:
0.0422
Gnomad4 FIN
AF:
0.0135
Gnomad4 NFE
AF:
0.0115
Gnomad4 OTH
AF:
0.0633
Alfa
AF:
0.0219
Hom.:
109
Bravo
AF:
0.0761

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.56
DANN
Benign
0.69

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: rs2366516; hg19: chrX-137060087; API