10-111851811-A-G

Variant summary

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

The ENST00000656217.1(ENSG00000287231):​n.133-62707T>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 0.462 in 152,014 control chromosomes in the GnomAD database, including 18,542 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 0.46 ( 18542 hom., cov: 32)

Consequence


ENST00000656217.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.164
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=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 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
ENST00000656217.1 linkuse as main transcriptn.133-62707T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.462
AC:
70149
AN:
151896
Hom.:
18490
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.722
Gnomad AMI
AF:
0.563
Gnomad AMR
AF:
0.379
Gnomad ASJ
AF:
0.312
Gnomad EAS
AF:
0.172
Gnomad SAS
AF:
0.183
Gnomad FIN
AF:
0.338
Gnomad MID
AF:
0.290
Gnomad NFE
AF:
0.392
Gnomad OTH
AF:
0.417
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.462
AC:
70265
AN:
152014
Hom.:
18542
Cov.:
32
AF XY:
0.451
AC XY:
33525
AN XY:
74280
show subpopulations
Gnomad4 AFR
AF:
0.722
Gnomad4 AMR
AF:
0.379
Gnomad4 ASJ
AF:
0.312
Gnomad4 EAS
AF:
0.172
Gnomad4 SAS
AF:
0.184
Gnomad4 FIN
AF:
0.338
Gnomad4 NFE
AF:
0.392
Gnomad4 OTH
AF:
0.412
Alfa
AF:
0.390
Hom.:
24969
Bravo
AF:
0.477
Asia WGS
AF:
0.237
AC:
823
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
5.3
DANN
Benign
0.42

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: rs959127; hg19: chr10-113611569; API