rs4140388

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.680-9962G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 152,048 control chromosomes in the GnomAD database, including 24,395 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 0.56 ( 24395 hom., cov: 33)

Consequence

ENSG00000246090
ENST00000500358.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.440
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=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC100507053NR_037884.1 linkuse as main transcriptn.680-9962G>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000246090ENST00000500358.6 linkuse as main transcriptn.680-9962G>C intron_variant 1
ADH4ENST00000504581.1 linkuse as main transcriptn.170-1803C>G intron_variant 3
ENSG00000246090ENST00000661393.1 linkuse as main transcriptn.676+10778G>C intron_variant

Frequencies

GnomAD3 genomes
AF:
0.560
AC:
85098
AN:
151930
Hom.:
24368
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.631
Gnomad AMI
AF:
0.430
Gnomad AMR
AF:
0.611
Gnomad ASJ
AF:
0.487
Gnomad EAS
AF:
0.265
Gnomad SAS
AF:
0.560
Gnomad FIN
AF:
0.596
Gnomad MID
AF:
0.547
Gnomad NFE
AF:
0.528
Gnomad OTH
AF:
0.543
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.560
AC:
85178
AN:
152048
Hom.:
24395
Cov.:
33
AF XY:
0.564
AC XY:
41904
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.631
Gnomad4 AMR
AF:
0.612
Gnomad4 ASJ
AF:
0.487
Gnomad4 EAS
AF:
0.264
Gnomad4 SAS
AF:
0.561
Gnomad4 FIN
AF:
0.596
Gnomad4 NFE
AF:
0.528
Gnomad4 OTH
AF:
0.546
Alfa
AF:
0.545
Hom.:
2831
Bravo
AF:
0.564
Asia WGS
AF:
0.522
AC:
1818
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.77
DANN
Benign
0.36

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: rs4140388; hg19: chr4-100065734; API