rs764892787

Variant names:

• chr5-158708039-C-G
• rs764892787
• NM_024007.5:c.1684G>C

Your query was ambiguous. Multiple possible variants found:

• chr5-158708039-C-G
• chr5-158708039-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_024007.5(EBF1):​c.1684G>C​(p.Val562Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V562I) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: EBF1 NM_024007.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.91

Genes affected

EBF1 (HGNC:3126): (EBF transcription factor 1) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of transcription, DNA-templated. Predicted to be located in nucleus. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.30738264).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EBF1	NM_024007.5	c.1684G>C	p.Val562Leu	missense_variant	Exon 15 of 16	ENST00000313708.11	NP_076870.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EBF1	ENST00000313708.11	c.1684G>C	p.Val562Leu	missense_variant	Exon 15 of 16	1	NM_024007.5	ENSP00000322898.6

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.29
BayesDel_addAF	Uncertain	0.028	T
BayesDel_noAF	Benign	-0.20
CADD	Pathogenic	26
DANN	Benign	0.96
DEOGEN2	Benign	0.16	.;T;.;.
Eigen	Benign	-0.027
Eigen_PC	Benign	0.16
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.78	T;D;D;D
M_CAP	Benign	0.018	T
MetaRNN	Benign	0.31	T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.4	.;L;.;.
PrimateAI	Pathogenic	0.82	D
PROVEAN	Benign	-0.90	.;N;N;N
REVEL	Benign	0.13
Sift	Benign	0.46	.;T;T;T
Sift4G	Benign	0.58	T;T;T;T
Polyphen		0.0	.;B;B;.
Vest4		0.71, 0.65, 0.67
MutPred		0.19		.;Loss of sheet (P = 0.1158);.;.;
MVP		0.71
MPC		0.42
ClinPred		0.88	D
GERP RS		5.1
Varity_R		0.15
gMVP		0.67

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

Other links and lift over

dbSNP: rs764892787; hg19: chr5-158135047;