3-176312308-G-T

Variant summary

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

The ENST00000687649.1(ENSG00000288895):​n.413+6120C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 151,938 control chromosomes in the GnomAD database, including 22,247 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 0.53 ( 22247 hom., cov: 32)

Consequence

ENSG00000288895
ENST00000687649.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.695
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=-0.95).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000288895ENST00000687649.1 linkn.413+6120C>A intron_variant Intron 3 of 4

Frequencies

GnomAD3 genomes
AF:
0.533
AC:
80976
AN:
151818
Hom.:
22244
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.422
Gnomad AMI
AF:
0.523
Gnomad AMR
AF:
0.483
Gnomad ASJ
AF:
0.553
Gnomad EAS
AF:
0.367
Gnomad SAS
AF:
0.454
Gnomad FIN
AF:
0.721
Gnomad MID
AF:
0.430
Gnomad NFE
AF:
0.601
Gnomad OTH
AF:
0.537
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.533
AC:
81015
AN:
151938
Hom.:
22247
Cov.:
32
AF XY:
0.536
AC XY:
39790
AN XY:
74240
show subpopulations
Gnomad4 AFR
AF:
0.422
Gnomad4 AMR
AF:
0.483
Gnomad4 ASJ
AF:
0.553
Gnomad4 EAS
AF:
0.367
Gnomad4 SAS
AF:
0.454
Gnomad4 FIN
AF:
0.721
Gnomad4 NFE
AF:
0.601
Gnomad4 OTH
AF:
0.533
Alfa
AF:
0.572
Hom.:
56955
Bravo
AF:
0.511

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.13
DANN
Benign
0.40

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: rs6799767; hg19: chr3-176030096; API