rs10484514

Variant summary

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

The ENST00000659063.1(ENSG00000288696):​n.43-32768C>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 0.192 in 152,098 control chromosomes in the GnomAD database, including 2,894 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 0.19 ( 2894 hom., cov: 32)

Consequence


ENST00000659063.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0620
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=-1.04).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105378102XR_943213.4 linkuse as main transcriptn.558+55842C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000659063.1 linkuse as main transcriptn.43-32768C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.192
AC:
29137
AN:
151980
Hom.:
2896
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.137
Gnomad AMI
AF:
0.126
Gnomad AMR
AF:
0.181
Gnomad ASJ
AF:
0.207
Gnomad EAS
AF:
0.205
Gnomad SAS
AF:
0.165
Gnomad FIN
AF:
0.177
Gnomad MID
AF:
0.228
Gnomad NFE
AF:
0.230
Gnomad OTH
AF:
0.203
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.192
AC:
29135
AN:
152098
Hom.:
2894
Cov.:
32
AF XY:
0.190
AC XY:
14092
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.137
Gnomad4 AMR
AF:
0.181
Gnomad4 ASJ
AF:
0.207
Gnomad4 EAS
AF:
0.204
Gnomad4 SAS
AF:
0.166
Gnomad4 FIN
AF:
0.177
Gnomad4 NFE
AF:
0.230
Gnomad4 OTH
AF:
0.202
Alfa
AF:
0.200
Hom.:
481
Bravo
AF:
0.188
Asia WGS
AF:
0.151
AC:
525
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.7
DANN
Benign
0.36

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: rs10484514; hg19: chr6-164396788; API