19-35318897-A-G

Variant summary

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

The ENST00000700969.1(ENSG00000289845):​n.144+8T>C variant causes a splice region, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 151,986 control chromosomes in the GnomAD database, including 51,230 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 0.82 ( 51230 hom., cov: 29)

Consequence


ENST00000700969.1 splice_region, intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0510
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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 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
ENST00000700969.1 linkuse as main transcriptn.144+8T>C splice_region_variant, intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.816
AC:
123922
AN:
151868
Hom.:
51165
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.949
Gnomad AMI
AF:
0.821
Gnomad AMR
AF:
0.799
Gnomad ASJ
AF:
0.790
Gnomad EAS
AF:
0.815
Gnomad SAS
AF:
0.845
Gnomad FIN
AF:
0.726
Gnomad MID
AF:
0.883
Gnomad NFE
AF:
0.751
Gnomad OTH
AF:
0.837
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.816
AC:
124050
AN:
151986
Hom.:
51230
Cov.:
29
AF XY:
0.816
AC XY:
60594
AN XY:
74242
show subpopulations
Gnomad4 AFR
AF:
0.950
Gnomad4 AMR
AF:
0.799
Gnomad4 ASJ
AF:
0.790
Gnomad4 EAS
AF:
0.815
Gnomad4 SAS
AF:
0.845
Gnomad4 FIN
AF:
0.726
Gnomad4 NFE
AF:
0.751
Gnomad4 OTH
AF:
0.838
Alfa
AF:
0.772
Hom.:
49885
Bravo
AF:
0.824
Asia WGS
AF:
0.863
AC:
3003
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
1.5
DANN
Benign
0.61

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: rs756796; hg19: chr19-35809800; API