10-63917874-C-T

Variant summary

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

The ENST00000654191.1(ENSG00000228566):​n.407+44898C>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 0.6 in 151,932 control chromosomes in the GnomAD database, including 27,673 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 0.60 ( 27673 hom., cov: 31)

Consequence


ENST00000654191.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0840
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=-0.72).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124902439XR_007062161.1 linkuse as main transcriptn.388+44898C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000654191.1 linkuse as main transcriptn.407+44898C>T intron_variant, non_coding_transcript_variant
ENST00000444770.1 linkuse as main transcriptn.495-72395C>T intron_variant, non_coding_transcript_variant 3
ENST00000660795.1 linkuse as main transcriptn.156+30786C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.600
AC:
91126
AN:
151814
Hom.:
27645
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.507
Gnomad AMI
AF:
0.486
Gnomad AMR
AF:
0.698
Gnomad ASJ
AF:
0.713
Gnomad EAS
AF:
0.644
Gnomad SAS
AF:
0.571
Gnomad FIN
AF:
0.639
Gnomad MID
AF:
0.693
Gnomad NFE
AF:
0.622
Gnomad OTH
AF:
0.641
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.600
AC:
91201
AN:
151932
Hom.:
27673
Cov.:
31
AF XY:
0.603
AC XY:
44773
AN XY:
74240
show subpopulations
Gnomad4 AFR
AF:
0.507
Gnomad4 AMR
AF:
0.698
Gnomad4 ASJ
AF:
0.713
Gnomad4 EAS
AF:
0.645
Gnomad4 SAS
AF:
0.572
Gnomad4 FIN
AF:
0.639
Gnomad4 NFE
AF:
0.622
Gnomad4 OTH
AF:
0.643
Alfa
AF:
0.631
Hom.:
40844
Bravo
AF:
0.602
Asia WGS
AF:
0.584
AC:
2029
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.72
CADD
Benign
1.8
DANN
Benign
0.80

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: rs2244205; hg19: chr10-65677634; API