rs10518498

Variant summary

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

The ENST00000661809.1(ENSG00000286251):​n.149-110580T>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 0.0397 in 152,096 control chromosomes in the GnomAD database, including 202 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 0.040 ( 202 hom., cov: 32)

Consequence


ENST00000661809.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.148
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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0619 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000661809.1 linkuse as main transcriptn.149-110580T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0398
AC:
6046
AN:
151978
Hom.:
201
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00959
Gnomad AMI
AF:
0.0978
Gnomad AMR
AF:
0.0128
Gnomad ASJ
AF:
0.0228
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0153
Gnomad FIN
AF:
0.0794
Gnomad MID
AF:
0.0285
Gnomad NFE
AF:
0.0635
Gnomad OTH
AF:
0.0234
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0397
AC:
6045
AN:
152096
Hom.:
202
Cov.:
32
AF XY:
0.0394
AC XY:
2927
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.00958
Gnomad4 AMR
AF:
0.0126
Gnomad4 ASJ
AF:
0.0228
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0153
Gnomad4 FIN
AF:
0.0794
Gnomad4 NFE
AF:
0.0635
Gnomad4 OTH
AF:
0.0232
Alfa
AF:
0.0517
Hom.:
136
Bravo
AF:
0.0335
Asia WGS
AF:
0.00810
AC:
28
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
8.5
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: rs10518498; hg19: chr4-127496877; API