rs2332056

Variant names:

• chr3-121879450-A-G
• rs2332056
• NM_018456.6:c.736+6662A>G

Variant summary

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

The NM_018456.6(EAF2):​c.736+6662A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,986 control chromosomes in the GnomAD database, including 5,194 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 0.25 (5194 hom., cov: 32)
• Consequence: EAF2 NM_018456.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 3 publications found

Genes affected

EAF2 (HGNC:23115): (ELL associated factor 2) Enables transcription elongation regulator activity. Involved in positive regulation of transcription by RNA polymerase II and regulation of transcription elongation from RNA polymerase II promoter. Part of transcription elongation factor complex. Biomarker of prostate cancer. [provided by Alliance of Genome Resources, Apr 2022]

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 (SAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EAF2	NM_018456.6	c.736+6662A>G		intron_variant	Intron 5 of 5	ENST00000273668.7	NP_060926.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EAF2	ENST00000273668.7	c.736+6662A>G		intron_variant	Intron 5 of 5	1	NM_018456.6	ENSP00000273668.2
EAF2	ENST00000490434.5	n.*392+6662A>G		intron_variant	Intron 4 of 4	1		ENSP00000418374.1

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38438 AN: 151868 Hom.: 5182 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.260

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.253 AC: 38483 AN: 151986 Hom.: 5194 Cov.: 32 AF XY: 0.256 AC XY: 19003 AN XY: 74312

African (AFR) AF: 0.318 AC: 13203 AN: 41462

American (AMR) AF: 0.262 AC: 3992 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3466

East Asian (EAS) AF: 0.158 AC: 818 AN: 5184

South Asian (SAS) AF: 0.390 AC: 1883 AN: 4824

European-Finnish (FIN) AF: 0.211 AC: 2219 AN: 10526

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14835 AN: 67942

Other (OTH) AF: 0.257 AC: 543 AN: 2114

Alfa AF: 0.255 Hom.: 839

Bravo AF: 0.256

Asia WGS AF: 0.302 AC: 1046 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.72
PhyloP100		0.24
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: rs2332056; hg19: chr3-121598297;