rs10483466

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000634305.1(ENSG00000283098):​n.251-895T>C 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 0.0561 in 152,276 control chromosomes in the GnomAD database, including 516 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 0.056 ( 516 hom., cov: 32)

Consequence


ENST00000634305.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.354
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000634305.1 linkuse as main transcriptn.251-895T>C intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.0561
AC:
8537
AN:
152158
Hom.:
511
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0307
Gnomad AMI
AF:
0.0515
Gnomad AMR
AF:
0.128
Gnomad ASJ
AF:
0.00202
Gnomad EAS
AF:
0.320
Gnomad SAS
AF:
0.0412
Gnomad FIN
AF:
0.0927
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.0340
Gnomad OTH
AF:
0.0482
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0561
AC:
8548
AN:
152276
Hom.:
516
Cov.:
32
AF XY:
0.0626
AC XY:
4662
AN XY:
74460
show subpopulations
Gnomad4 AFR
AF:
0.0306
Gnomad4 AMR
AF:
0.128
Gnomad4 ASJ
AF:
0.00202
Gnomad4 EAS
AF:
0.320
Gnomad4 SAS
AF:
0.0413
Gnomad4 FIN
AF:
0.0927
Gnomad4 NFE
AF:
0.0339
Gnomad4 OTH
AF:
0.0520
Alfa
AF:
0.0422
Hom.:
486
Bravo
AF:
0.0597
Asia WGS
AF:
0.178
AC:
619
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.39
CADD
Benign
17
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: rs10483466; hg19: chr14-36917076; API