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GeneBe

rs10483623

chr14-53623359-T-G

Variant summary

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

The ENST00000648066.1(ENSG00000237356):n.335-63840T>G 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 0.161 in 152,188 control chromosomes in the GnomAD database, including 2,143 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 0.16 ( 2143 hom., cov: 32)

Consequence


ENST00000648066.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.116
Variant links:
Genes affected

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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=-0.86).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105370504XR_943876.3 linkuse as main transcriptn.29701-63840T>G intron_variant, non_coding_transcript_variant
LOC105370504XR_001750974.1 linkuse as main transcriptn.3896-63840T>G intron_variant, non_coding_transcript_variant
LOC105370504XR_001750975.3 linkuse as main transcriptn.29701-63840T>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000648066.1 linkuse as main transcriptn.335-63840T>G intron_variant, non_coding_transcript_variant
ENST00000456100.6 linkuse as main transcriptn.326-63840T>G intron_variant, non_coding_transcript_variant 4
ENST00000663444.1 linkuse as main transcriptn.560-63840T>G intron_variant, non_coding_transcript_variant
ENST00000669612.1 linkuse as main transcriptn.398-63840T>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.161
AC:
24518
AN:
152070
Hom.:
2142
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0961
Gnomad AMI
AF:
0.423
Gnomad AMR
AF:
0.125
Gnomad ASJ
AF:
0.230
Gnomad EAS
AF:
0.0791
Gnomad SAS
AF:
0.167
Gnomad FIN
AF:
0.167
Gnomad MID
AF:
0.158
Gnomad NFE
AF:
0.206
Gnomad OTH
AF:
0.182
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:
0.161
AC:
24525
AN:
152188
Hom.:
2143
Cov.:
32
AF XY:
0.158
AC XY:
11754
AN XY:
74416
show subpopulations
Gnomad4 AFR
AF:
0.0962
Gnomad4 AMR
AF:
0.125
Gnomad4 ASJ
AF:
0.230
Gnomad4 EAS
AF:
0.0793
Gnomad4 SAS
AF:
0.167
Gnomad4 FIN
AF:
0.167
Gnomad4 NFE
AF:
0.206
Gnomad4 OTH
AF:
0.180
Alfa
AF:
0.195
Hom.:
1444
Bravo
AF:
0.156
Asia WGS
AF:
0.109
AC:
380
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
Cadd
Benign
0.95
Dann
Benign
0.31

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: rs10483623; hg19: chr14-54090077; API