6-1515139-A-G

Variant names:

• chr6-1515139-A-G
• rs3935776
• ENST00000404600.2:n.151T>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000404600.2(ELF2P2):​n.151T>C variant causes a non coding transcript exon change involving the alteration of a non-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.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ELF2P2 ENST00000404600.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.587
• Publications: 3 publications found

Genes affected

ELF2P2 (HGNC:24610):

ENSG00000305114 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELF2P2		n.1515139A>G		intragenic_variant
LOC102723944	XR_427861.4	n.235-12576T>C		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELF2P2	ENST00000404600.2	n.151T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000305114	ENST00000808839.1	n.567A>G		non_coding_transcript_exon_variant	Exon 4 of 5
ENSG00000305114	ENST00000808841.1	n.520A>G		non_coding_transcript_exon_variant	Exon 3 of 4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 12

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 24996

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	3.2
DANN	Benign	0.60
PhyloP100		0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3935776; hg19: chr6-1515374;