chr11-40110654-A-C

Variant summary

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

The ENST00000624239.1(ENSG00000279675):​n.1946T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 151,828 control chromosomes in the GnomAD database, including 17,969 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 0.47 ( 17969 hom., cov: 32)
Failed GnomAD Quality Control

Consequence


ENST00000624239.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.18
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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 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
ENST00000624239.1 linkuse as main transcriptn.1946T>G non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD3 genomes
AF:
0.468
AC:
71056
AN:
151710
Hom.:
17915
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.655
Gnomad AMI
AF:
0.565
Gnomad AMR
AF:
0.438
Gnomad ASJ
AF:
0.476
Gnomad EAS
AF:
0.624
Gnomad SAS
AF:
0.267
Gnomad FIN
AF:
0.299
Gnomad MID
AF:
0.434
Gnomad NFE
AF:
0.389
Gnomad OTH
AF:
0.482
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
0
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome
AF:
0.469
AC:
71174
AN:
151828
Hom.:
17969
Cov.:
32
AF XY:
0.463
AC XY:
34359
AN XY:
74222
show subpopulations
Gnomad4 AFR
AF:
0.655
Gnomad4 AMR
AF:
0.437
Gnomad4 ASJ
AF:
0.476
Gnomad4 EAS
AF:
0.624
Gnomad4 SAS
AF:
0.268
Gnomad4 FIN
AF:
0.299
Gnomad4 NFE
AF:
0.389
Gnomad4 OTH
AF:
0.485
Alfa
AF:
0.432
Hom.:
2416
Bravo
AF:
0.496
Asia WGS
AF:
0.468
AC:
1620
AN:
3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
3.2
DANN
Benign
0.80

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: rs1870874; hg19: chr11-40132204; COSMIC: COSV53419690; API