4-37062709-G-T

Variant summary

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

The variant allele was found at a frequency of 0.137 in 152,086 control chromosomes in the GnomAD database, including 1,994 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 0.14 ( 1994 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0100
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 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

Frequencies

GnomAD3 genomes
AF:
0.137
AC:
20795
AN:
151968
Hom.:
1999
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0539
Gnomad AMI
AF:
0.177
Gnomad AMR
AF:
0.201
Gnomad ASJ
AF:
0.193
Gnomad EAS
AF:
0.456
Gnomad SAS
AF:
0.283
Gnomad FIN
AF:
0.166
Gnomad MID
AF:
0.180
Gnomad NFE
AF:
0.130
Gnomad OTH
AF:
0.144
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.137
AC:
20790
AN:
152086
Hom.:
1994
Cov.:
32
AF XY:
0.144
AC XY:
10716
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.0538
Gnomad4 AMR
AF:
0.201
Gnomad4 ASJ
AF:
0.193
Gnomad4 EAS
AF:
0.455
Gnomad4 SAS
AF:
0.282
Gnomad4 FIN
AF:
0.166
Gnomad4 NFE
AF:
0.130
Gnomad4 OTH
AF:
0.146
Alfa
AF:
0.144
Hom.:
2184
Bravo
AF:
0.137
Asia WGS
AF:
0.331
AC:
1149
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.6
DANN
Benign
0.53

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: rs13117816; hg19: chr4-37064331; API