chr2-73291405-G-A

Variant summary

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

The NM_001965.4(EGR4):​c.*52C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,527,060 control chromosomes in the GnomAD database, including 15,401 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 0.18 ( 3886 hom., cov: 33)
Exomes 𝑓: 0.094 ( 11515 hom. )

Consequence

EGR4
NM_001965.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.623
Variant links:
Genes affected
EGR4 (HGNC:3241): (early growth response 4) Enables DNA-binding transcription activator activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
EGR4NM_001965.4 linkuse as main transcriptc.*52C>T 3_prime_UTR_variant 2/2 ENST00000436467.4
EGR4XM_047443603.1 linkuse as main transcriptc.*52C>T 3_prime_UTR_variant 2/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
EGR4ENST00000436467.4 linkuse as main transcriptc.*52C>T 3_prime_UTR_variant 2/21 NM_001965.4 P2
EGR4ENST00000545030.1 linkuse as main transcriptc.*52C>T 3_prime_UTR_variant 2/21 A2

Frequencies

GnomAD3 genomes
AF:
0.176
AC:
26737
AN:
152098
Hom.:
3873
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.365
Gnomad AMI
AF:
0.0626
Gnomad AMR
AF:
0.184
Gnomad ASJ
AF:
0.123
Gnomad EAS
AF:
0.423
Gnomad SAS
AF:
0.219
Gnomad FIN
AF:
0.0554
Gnomad MID
AF:
0.177
Gnomad NFE
AF:
0.0601
Gnomad OTH
AF:
0.167
GnomAD4 exome
AF:
0.0944
AC:
129848
AN:
1374842
Hom.:
11515
Cov.:
31
AF XY:
0.0963
AC XY:
64975
AN XY:
674382
show subpopulations
Gnomad4 AFR exome
AF:
0.378
Gnomad4 AMR exome
AF:
0.218
Gnomad4 ASJ exome
AF:
0.133
Gnomad4 EAS exome
AF:
0.441
Gnomad4 SAS exome
AF:
0.217
Gnomad4 FIN exome
AF:
0.0547
Gnomad4 NFE exome
AF:
0.0612
Gnomad4 OTH exome
AF:
0.123
GnomAD4 genome
AF:
0.176
AC:
26789
AN:
152218
Hom.:
3886
Cov.:
33
AF XY:
0.178
AC XY:
13223
AN XY:
74416
show subpopulations
Gnomad4 AFR
AF:
0.365
Gnomad4 AMR
AF:
0.184
Gnomad4 ASJ
AF:
0.123
Gnomad4 EAS
AF:
0.423
Gnomad4 SAS
AF:
0.220
Gnomad4 FIN
AF:
0.0554
Gnomad4 NFE
AF:
0.0601
Gnomad4 OTH
AF:
0.166
Alfa
AF:
0.124
Hom.:
353
Bravo
AF:
0.198
Asia WGS
AF:
0.323
AC:
1123
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
5.9
DANN
Benign
0.83

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: rs2229294; hg19: chr2-73518533; COSMIC: COSV71531991; API