rs2229294

Variant names:

• chr2-73291405-G-A
• rs2229294
• NM_001965.4:c.*52C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-73291405-G-A
• chr2-73291405-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.623
• Publications: 10 publications found

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]

ENSG00000310032 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001965.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EGR4	NM_001965.4	MANE Select	c.*52C>T		3_prime_UTR	Exon 2 of 2	NP_001956.4	A0A0C4DG96

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EGR4	ENST00000436467.4	TSL:1 MANE Select	c.*52C>T		3_prime_UTR	Exon 2 of 2	ENSP00000419687.1	A0A0C4DG96
	EGR4	ENST00000545030.1	TSL:1	c.*52C>T		3_prime_UTR	Exon 2 of 2	ENSP00000445626.1	Q05215
	EGR4	ENST00000858695.1		c.*52C>T		3_prime_UTR	Exon 2 of 2	ENSP00000528754.1

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26737 AN: 152098 Hom.: 3873 Cov.: 33

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

African (AFR) AF: 0.378 AC: 11565 AN: 30568

American (AMR) AF: 0.218 AC: 7008 AN: 32086

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 2758 AN: 20734

East Asian (EAS) AF: 0.441 AC: 17112 AN: 38782

South Asian (SAS) AF: 0.217 AC: 15582 AN: 71646

European-Finnish (FIN) AF: 0.0547 AC: 2674 AN: 48914

Middle Eastern (MID) AF: 0.145 AC: 632 AN: 4360

European-Non Finnish (NFE) AF: 0.0612 AC: 65542 AN: 1071264

Other (OTH) AF: 0.123 AC: 6975 AN: 56488

GnomAD4 genome AF: 0.176 AC: 26789 AN: 152218 Hom.: 3886 Cov.: 33 AF XY: 0.178 AC XY: 13223 AN XY: 74416

African (AFR) AF: 0.365 AC: 15169 AN: 41512

American (AMR) AF: 0.184 AC: 2819 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3472

East Asian (EAS) AF: 0.423 AC: 2176 AN: 5140

South Asian (SAS) AF: 0.220 AC: 1059 AN: 4820

European-Finnish (FIN) AF: 0.0554 AC: 589 AN: 10628

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.0601 AC: 4090 AN: 68024

Other (OTH) AF: 0.166 AC: 350 AN: 2112

Alfa AF: 0.131 Hom.: 404

Bravo AF: 0.198

Asia WGS AF: 0.323 AC: 1123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.9
DANN	Benign	0.83
PhyloP100		0.62
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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