rs3213180

Variant names:

• chr20-33675818-G-C
• rs3213180
• NM_005225.3:c.*914C>G

Your query was ambiguous. Multiple possible variants found:

• chr20-33675818-G-C
• chr20-33675818-G-T

Variant summary

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

The NM_005225.3(E2F1):​c.*914C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.084 in 185,128 control chromosomes in the GnomAD database, including 967 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 0.080 (749 hom., cov: 32)
  • Exomes 𝑓: 0.10 (218 hom.)
• Consequence: E2F1 NM_005225.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348
• Publications: 23 publications found

Genes affected

E2F1 (HGNC:3113): (E2F transcription factor 1) The protein encoded by this gene is a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cell cycle and action of tumor suppressor proteins and is also a target of the transforming proteins of small DNA tumor viruses. The E2F proteins contain several evolutionally conserved domains found in most members of the family. These domains include a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. This protein and another 2 members, E2F2 and E2F3, have an additional cyclin binding domain. This protein binds preferentially to retinoblastoma protein pRB in a cell-cycle dependent manner. It can mediate both cell proliferation and p53-dependent/independent apoptosis. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005225.3. 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
	E2F1	NM_005225.3	MANE Select	c.*914C>G		3_prime_UTR	Exon 7 of 7	NP_005216.1	Q01094

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	E2F1	ENST00000343380.6	TSL:1 MANE Select	c.*914C>G		3_prime_UTR	Exon 7 of 7	ENSP00000345571.5	Q01094
	E2F1	ENST00000932104.1		c.*914C>G		3_prime_UTR	Exon 7 of 7	ENSP00000602163.1
	E2F1	ENST00000932103.1		c.*914C>G		3_prime_UTR	Exon 7 of 7	ENSP00000602162.1

Frequencies

GnomAD3 genomes AF: 0.0802 AC: 12190 AN: 152046 Hom.: 749 Cov.: 32

Gnomad AFR AF: 0.0230

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.0795

Gnomad ASJ AF: 0.0749

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0970

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0930

Gnomad OTH AF: 0.0541

GnomAD4 exome AF: 0.102 AC: 3364 AN: 32964 Hom.: 218 Cov.: 0 AF XY: 0.101 AC XY: 1734 AN XY: 17220

African (AFR) AF: 0.0191 AC: 14 AN: 734

American (AMR) AF: 0.0470 AC: 33 AN: 702

Ashkenazi Jewish (ASJ) AF: 0.0784 AC: 85 AN: 1084

East Asian (EAS) AF: 0.273 AC: 867 AN: 3180

South Asian (SAS) AF: 0.120 AC: 33 AN: 274

European-Finnish (FIN) AF: 0.0799 AC: 325 AN: 4070

Middle Eastern (MID) AF: 0.0476 AC: 8 AN: 168

European-Non Finnish (NFE) AF: 0.0875 AC: 1827 AN: 20880

Other (OTH) AF: 0.0919 AC: 172 AN: 1872

GnomAD4 genome AF: 0.0801 AC: 12187 AN: 152164 Hom.: 749 Cov.: 32 AF XY: 0.0819 AC XY: 6090 AN XY: 74350

African (AFR) AF: 0.0229 AC: 951 AN: 41534

American (AMR) AF: 0.0795 AC: 1216 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0749 AC: 260 AN: 3472

East Asian (EAS) AF: 0.317 AC: 1628 AN: 5142

South Asian (SAS) AF: 0.128 AC: 618 AN: 4824

European-Finnish (FIN) AF: 0.0970 AC: 1027 AN: 10592

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0930 AC: 6324 AN: 67986

Other (OTH) AF: 0.0536 AC: 113 AN: 2110

Alfa AF: 0.0439 Hom.: 30

Bravo AF: 0.0757

Asia WGS AF: 0.185 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.9
DANN	Benign	0.49
PhyloP100		0.35
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs3213180; hg19: chr20-32263624;