5-138468946-T-C

Variant summary

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

The NM_001964.3(EGR1):​c.*865T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0389 in 152,334 control chromosomes in the GnomAD database, including 200 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 0.039 ( 199 hom., cov: 31)
Exomes 𝑓: 0.017 ( 1 hom. )

Consequence

EGR1
NM_001964.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0110
Variant links:
Genes affected
EGR1 (HGNC:3238): (early growth response 1) The protein encoded by this gene belongs to the EGR family of C2H2-type zinc-finger proteins. It is a nuclear protein and functions as a transcriptional regulator. The products of target genes it activates are required for differentitation and mitogenesis. Studies suggest this is a cancer suppressor gene. [provided by RefSeq, Dec 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0608 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
EGR1NM_001964.3 linkuse as main transcriptc.*865T>C 3_prime_UTR_variant 2/2 ENST00000239938.5 NP_001955.1 P18146Q546S1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
EGR1ENST00000239938.5 linkuse as main transcriptc.*865T>C 3_prime_UTR_variant 2/21 NM_001964.3 ENSP00000239938.4 P18146

Frequencies

GnomAD3 genomes
AF:
0.0390
AC:
5924
AN:
151806
Hom.:
199
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0117
Gnomad AMI
AF:
0.0175
Gnomad AMR
AF:
0.0422
Gnomad ASJ
AF:
0.0596
Gnomad EAS
AF:
0.000773
Gnomad SAS
AF:
0.0198
Gnomad FIN
AF:
0.0152
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.0624
Gnomad OTH
AF:
0.0345
GnomAD4 exome
AF:
0.0171
AC:
7
AN:
410
Hom.:
1
Cov.:
0
AF XY:
0.0282
AC XY:
7
AN XY:
248
show subpopulations
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0177
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0390
AC:
5922
AN:
151924
Hom.:
199
Cov.:
31
AF XY:
0.0359
AC XY:
2664
AN XY:
74262
show subpopulations
Gnomad4 AFR
AF:
0.0117
Gnomad4 AMR
AF:
0.0422
Gnomad4 ASJ
AF:
0.0596
Gnomad4 EAS
AF:
0.000775
Gnomad4 SAS
AF:
0.0196
Gnomad4 FIN
AF:
0.0152
Gnomad4 NFE
AF:
0.0624
Gnomad4 OTH
AF:
0.0342
Alfa
AF:
0.0530
Hom.:
70
Bravo
AF:
0.0409
Asia WGS
AF:
0.00866
AC:
30
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
4.2
DANN
Benign
0.63

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: rs6914; hg19: chr5-137804635; API