6-1514564-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000404600.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELF2P2	ENST00000404600.2	TSL:6	n.726G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000305114	ENST00000808839.1		n.399-407C>T		intron	N/A
	ENSG00000305114	ENST00000808841.1		n.352-407C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9328058;

hg19: chr6-1514799;