4-119322356-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The variant allele was found at a frequency of 0.566 in 386,000 control chromosomes in the GnomAD database, including 62,260 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.57 ( 24456 hom., cov: 32)
Exomes 𝑓: 0.57 ( 37804 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.598
Variant links:

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ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 4-119322356-T-C is Benign according to our data. Variant chr4-119322356-T-C is described in ClinVar as [Benign]. Clinvar id is 1268685.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 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

Frequencies

GnomAD3 genomes
AF:
0.567
AC:
86053
AN:
151814
Hom.:
24423
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.559
Gnomad AMI
AF:
0.449
Gnomad AMR
AF:
0.605
Gnomad ASJ
AF:
0.621
Gnomad EAS
AF:
0.629
Gnomad SAS
AF:
0.533
Gnomad FIN
AF:
0.512
Gnomad MID
AF:
0.564
Gnomad NFE
AF:
0.568
Gnomad OTH
AF:
0.596
GnomAD4 exome
AF:
0.566
AC:
132408
AN:
234068
Hom.:
37804
Cov.:
0
AF XY:
0.565
AC XY:
67952
AN XY:
120234
show subpopulations
Gnomad4 AFR exome
AF:
0.561
Gnomad4 AMR exome
AF:
0.630
Gnomad4 ASJ exome
AF:
0.635
Gnomad4 EAS exome
AF:
0.549
Gnomad4 SAS exome
AF:
0.524
Gnomad4 FIN exome
AF:
0.512
Gnomad4 NFE exome
AF:
0.567
Gnomad4 OTH exome
AF:
0.588
GnomAD4 genome
AF:
0.567
AC:
86151
AN:
151932
Hom.:
24456
Cov.:
32
AF XY:
0.564
AC XY:
41868
AN XY:
74244
show subpopulations
Gnomad4 AFR
AF:
0.559
Gnomad4 AMR
AF:
0.605
Gnomad4 ASJ
AF:
0.621
Gnomad4 EAS
AF:
0.628
Gnomad4 SAS
AF:
0.533
Gnomad4 FIN
AF:
0.512
Gnomad4 NFE
AF:
0.568
Gnomad4 OTH
AF:
0.599
Alfa
AF:
0.564
Hom.:
3126
Bravo
AF:
0.579
Asia WGS
AF:
0.634
AC:
2206
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxNov 11, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
3.4
DANN
Benign
0.33

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs6857641; hg19: chr4-120243511; COSMIC: COSV56789133; API