11-95585996-G-A

Variant summary

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

The ENST00000648353.1(ENSG00000285842):​n.525+13788G>A 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 0.285 in 151,554 control chromosomes in the GnomAD database, including 6,354 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 0.28 ( 6354 hom., cov: 31)

Consequence


ENST00000648353.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.291
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=-0.91).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.401 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
ENST00000648353.1 linkuse as main transcriptn.525+13788G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.285
AC:
43119
AN:
151436
Hom.:
6338
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.289
Gnomad AMI
AF:
0.243
Gnomad AMR
AF:
0.408
Gnomad ASJ
AF:
0.202
Gnomad EAS
AF:
0.394
Gnomad SAS
AF:
0.311
Gnomad FIN
AF:
0.253
Gnomad MID
AF:
0.231
Gnomad NFE
AF:
0.254
Gnomad OTH
AF:
0.278
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.285
AC:
43180
AN:
151554
Hom.:
6354
Cov.:
31
AF XY:
0.288
AC XY:
21300
AN XY:
74034
show subpopulations
Gnomad4 AFR
AF:
0.289
Gnomad4 AMR
AF:
0.409
Gnomad4 ASJ
AF:
0.202
Gnomad4 EAS
AF:
0.396
Gnomad4 SAS
AF:
0.311
Gnomad4 FIN
AF:
0.253
Gnomad4 NFE
AF:
0.254
Gnomad4 OTH
AF:
0.281
Alfa
AF:
0.201
Hom.:
592
Asia WGS
AF:
0.375
AC:
1300
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.58
DANN
Benign
0.83

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: rs1255537; hg19: chr11-95319160; COSMIC: COSV70883306; API