rs10516537

Variant summary

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

The ENST00000650850.1(ENSG00000286147):​n.319-424A>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 0.844 in 152,026 control chromosomes in the GnomAD database, including 54,345 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 0.84 ( 54345 hom., cov: 31)

Consequence


ENST00000650850.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.189
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=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105377356XR_939051.1 linkuse as main transcriptn.261-424A>C intron_variant, non_coding_transcript_variant
LOC105377356XR_939053.3 linkuse as main transcriptn.261-424A>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000650850.1 linkuse as main transcriptn.319-424A>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.844
AC:
128201
AN:
151908
Hom.:
54316
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.778
Gnomad AMI
AF:
0.932
Gnomad AMR
AF:
0.887
Gnomad ASJ
AF:
0.864
Gnomad EAS
AF:
0.937
Gnomad SAS
AF:
0.896
Gnomad FIN
AF:
0.921
Gnomad MID
AF:
0.854
Gnomad NFE
AF:
0.849
Gnomad OTH
AF:
0.851
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.844
AC:
128279
AN:
152026
Hom.:
54345
Cov.:
31
AF XY:
0.850
AC XY:
63209
AN XY:
74320
show subpopulations
Gnomad4 AFR
AF:
0.778
Gnomad4 AMR
AF:
0.887
Gnomad4 ASJ
AF:
0.864
Gnomad4 EAS
AF:
0.937
Gnomad4 SAS
AF:
0.895
Gnomad4 FIN
AF:
0.921
Gnomad4 NFE
AF:
0.849
Gnomad4 OTH
AF:
0.853
Alfa
AF:
0.853
Hom.:
66235
Bravo
AF:
0.841
Asia WGS
AF:
0.885
AC:
3073
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.1
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: rs10516537; hg19: chr4-107628071; API