Genetic Variant ELF2P2:n.151T>A (chr6-1515139-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000404600.2(ELF2P2):n.151T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000121 in 823,070 control chromosomes in the GnomAD database, with no homozygous occurrence. 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)

Exomes 𝑓: 0.0000012 ( 0 hom. )

Consequence

ELF2P2
ENST00000404600.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.587

Publications

3 publications found

Variant links:

Genes affected

ELF2P2 (HGNC:24610):

ELF2P2 links:

ENSG00000305114 (HGNC:):

ENSG00000305114 links:

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ACMG classification

Classification was made for transcript

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>T		intragenic_variant
LOC102723944	XR_427861.4 link	n.235-12576T>A		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ELF2P2	ENST00000404600.2 link	n.151T>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000305114	ENST00000808839.1 link	n.567A>T	non_coding_transcript_exon_variant	Exon 4 of 5
ENSG00000305114	ENST00000808841.1 link	n.520A>T	non_coding_transcript_exon_variant	Exon 3 of 4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000121

AC:

AN:

823070

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

433180

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

20662

American (AMR)

AF:

0.00

AC:

AN:

42694

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

21062

East Asian (EAS)

AF:

0.00

AC:

AN:

33818

South Asian (SAS)

AF:

0.00

AC:

AN:

74020

European-Finnish (FIN)

AF:

0.00

AC:

AN:

49922

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4356

European-Non Finnish (NFE)

AF:

0.00000186

AC:

AN:

538758

Other (OTH)

AF:

0.00

AC:

AN:

37778

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

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

2.7

(source)

DANN

Benign

0.68

PhyloP100

0.59

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over