rs899101

Variant summary

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

The ENST00000654829.1(ENSG00000267284):​n.304-613T>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 0.263 in 152,178 control chromosomes in the GnomAD database, including 5,829 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 0.26 ( 5829 hom., cov: 33)

Consequence


ENST00000654829.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.790
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=-0.97).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105372130XR_007066382.1 linkuse as main transcriptn.476-613T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000654829.1 linkuse as main transcriptn.304-613T>C intron_variant, non_coding_transcript_variant
ENST00000589662.1 linkuse as main transcriptn.365-613T>C intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.263
AC:
39978
AN:
152060
Hom.:
5823
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.142
Gnomad AMI
AF:
0.286
Gnomad AMR
AF:
0.383
Gnomad ASJ
AF:
0.271
Gnomad EAS
AF:
0.178
Gnomad SAS
AF:
0.175
Gnomad FIN
AF:
0.273
Gnomad MID
AF:
0.209
Gnomad NFE
AF:
0.320
Gnomad OTH
AF:
0.267
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.263
AC:
40024
AN:
152178
Hom.:
5829
Cov.:
33
AF XY:
0.262
AC XY:
19526
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.143
Gnomad4 AMR
AF:
0.383
Gnomad4 ASJ
AF:
0.271
Gnomad4 EAS
AF:
0.178
Gnomad4 SAS
AF:
0.175
Gnomad4 FIN
AF:
0.273
Gnomad4 NFE
AF:
0.320
Gnomad4 OTH
AF:
0.268
Alfa
AF:
0.269
Hom.:
827
Bravo
AF:
0.267
Asia WGS
AF:
0.210
AC:
729
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.48
DANN
Benign
0.28

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: rs899101; hg19: chr18-53455231; API