chr6-1514564-C-T

Variant names:

• chr6-1514564-C-T
• rs9328058
• ENST00000404600.2:n.726G>A

Variant summary

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

The ENST00000404600.2(ELF2P2):​n.726G>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 0.398 in 1,528,490 control chromosomes in the GnomAD database, including 125,386 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 0.43 (15027 hom., cov: 33)
  • Exomes 𝑓: 0.39 (110359 hom.)
• Consequence: ELF2P2 ENST00000404600.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 4 publications found

Genes affected

ELF2P2 (HGNC:24610):

ENSG00000305114 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELF2P2		n.1514564C>T		intragenic_variant
LOC102723944	XR_427861.4	n.235-12001G>A		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELF2P2	ENST00000404600.2	n.726G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000305114	ENST00000808839.1	n.399-407C>T		intron_variant	Intron 3 of 4
ENSG00000305114	ENST00000808841.1	n.352-407C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65949 AN: 151902 Hom.: 14996 Cov.: 33

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.431

GnomAD4 exome AF: 0.394 AC: 542337 AN: 1376470 Hom.: 110359 Cov.: 30 AF XY: 0.397 AC XY: 270299 AN XY: 680880

African (AFR) AF: 0.541 AC: 16499 AN: 30518

American (AMR) AF: 0.297 AC: 9609 AN: 32400

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 9075 AN: 21432

East Asian (EAS) AF: 0.688 AC: 27003 AN: 39258

South Asian (SAS) AF: 0.494 AC: 36074 AN: 72970

European-Finnish (FIN) AF: 0.415 AC: 20882 AN: 50342

Middle Eastern (MID) AF: 0.502 AC: 2666 AN: 5310

European-Non Finnish (NFE) AF: 0.372 AC: 396679 AN: 1067388

Other (OTH) AF: 0.420 AC: 23850 AN: 56852

GnomAD4 genome AF: 0.434 AC: 66036 AN: 152020 Hom.: 15027 Cov.: 33 AF XY: 0.438 AC XY: 32566 AN XY: 74288

African (AFR) AF: 0.529 AC: 21910 AN: 41444

American (AMR) AF: 0.345 AC: 5266 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1446 AN: 3470

East Asian (EAS) AF: 0.710 AC: 3675 AN: 5174

South Asian (SAS) AF: 0.511 AC: 2459 AN: 4812

European-Finnish (FIN) AF: 0.416 AC: 4392 AN: 10550

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25521 AN: 67972

Other (OTH) AF: 0.433 AC: 914 AN: 2112

Alfa AF: 0.400 Hom.: 13622

Bravo AF: 0.435

Asia WGS AF: 0.563 AC: 1955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	8.4
DANN	Benign	0.65
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs9328058; hg19: chr6-1514799;