rs17842780

Variant summary

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

The ENST00000657494.1(ENSG00000287682):​n.226+1488A>G 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 0.255 in 152,132 control chromosomes in the GnomAD database, including 5,170 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 ( 5170 hom., cov: 32)

Consequence


ENST00000657494.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.35
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=-0.93).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000657494.1 linkuse as main transcriptn.226+1488A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.255
AC:
38752
AN:
152014
Hom.:
5158
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.245
Gnomad AMI
AF:
0.178
Gnomad AMR
AF:
0.341
Gnomad ASJ
AF:
0.199
Gnomad EAS
AF:
0.0939
Gnomad SAS
AF:
0.247
Gnomad FIN
AF:
0.282
Gnomad MID
AF:
0.241
Gnomad NFE
AF:
0.254
Gnomad OTH
AF:
0.258
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.255
AC:
38802
AN:
152132
Hom.:
5170
Cov.:
32
AF XY:
0.256
AC XY:
19040
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.245
Gnomad4 AMR
AF:
0.341
Gnomad4 ASJ
AF:
0.199
Gnomad4 EAS
AF:
0.0941
Gnomad4 SAS
AF:
0.247
Gnomad4 FIN
AF:
0.282
Gnomad4 NFE
AF:
0.254
Gnomad4 OTH
AF:
0.264
Alfa
AF:
0.252
Hom.:
9867
Bravo
AF:
0.260
Asia WGS
AF:
0.217
AC:
755
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.32
DANN
Benign
0.44

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: rs17842780; hg19: chr3-101607164; COSMIC: COSV53460789; API