rs199055

Variant summary

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

The ENST00000690652.2(ENSG00000289368):​n.211-32219T>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 0.0605 in 152,178 control chromosomes in the GnomAD database, including 472 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 0.060 ( 472 hom., cov: 31)

Consequence


ENST00000690652.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.363
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC105374976XR_001744046.2 linkuse as main transcriptn.401-32219T>C intron_variant, non_coding_transcript_variant
LOC105374976XR_007059501.1 linkuse as main transcriptn.379-32219T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000690652.2 linkuse as main transcriptn.211-32219T>C intron_variant, non_coding_transcript_variant
ENST00000700866.1 linkuse as main transcriptn.181-32219T>C intron_variant, non_coding_transcript_variant
ENST00000702216.1 linkuse as main transcriptn.203-32219T>C intron_variant, non_coding_transcript_variant
ENST00000702386.1 linkuse as main transcriptn.200-32219T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0604
AC:
9178
AN:
152058
Hom.:
468
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.113
Gnomad AMI
AF:
0.0219
Gnomad AMR
AF:
0.0591
Gnomad ASJ
AF:
0.0531
Gnomad EAS
AF:
0.230
Gnomad SAS
AF:
0.103
Gnomad FIN
AF:
0.0286
Gnomad MID
AF:
0.0696
Gnomad NFE
AF:
0.0186
Gnomad OTH
AF:
0.0627
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0605
AC:
9201
AN:
152178
Hom.:
472
Cov.:
31
AF XY:
0.0631
AC XY:
4698
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.113
Gnomad4 AMR
AF:
0.0592
Gnomad4 ASJ
AF:
0.0531
Gnomad4 EAS
AF:
0.230
Gnomad4 SAS
AF:
0.102
Gnomad4 FIN
AF:
0.0286
Gnomad4 NFE
AF:
0.0186
Gnomad4 OTH
AF:
0.0620
Alfa
AF:
0.0299
Hom.:
287
Bravo
AF:
0.0664
Asia WGS
AF:
0.131
AC:
455
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.2
DANN
Benign
0.35

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: rs199055; hg19: chr6-23490117; API