rs3935776

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-1515139-A-C
• chr6-1515139-A-G
• chr6-1515139-A-T

Variant summary

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

The ENST00000404600.2(ELF2P2):​n.151T>G 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 0.254 in 969,770 control chromosomes in the GnomAD database, including 33,008 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 0.29 (6791 hom., cov: 33)
  • Exomes 𝑓: 0.25 (26217 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44745 AN: 151910 Hom.: 6788 Cov.: 33

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.302

GnomAD4 exome AF: 0.246 AC: 201181 AN: 817742 Hom.: 26217 Cov.: 12 AF XY: 0.250 AC XY: 107764 AN XY: 430560

African (AFR) AF: 0.326 AC: 6688 AN: 20526

American (AMR) AF: 0.242 AC: 10318 AN: 42662

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 5573 AN: 21024

East Asian (EAS) AF: 0.350 AC: 11813 AN: 33720

South Asian (SAS) AF: 0.290 AC: 21468 AN: 73932

European-Finnish (FIN) AF: 0.213 AC: 10612 AN: 49814

Middle Eastern (MID) AF: 0.333 AC: 1443 AN: 4338

European-Non Finnish (NFE) AF: 0.231 AC: 123307 AN: 534128

Other (OTH) AF: 0.265 AC: 9959 AN: 37598

GnomAD4 genome AF: 0.295 AC: 44778 AN: 152028 Hom.: 6791 Cov.: 33 AF XY: 0.292 AC XY: 21731 AN XY: 74306

African (AFR) AF: 0.356 AC: 14763 AN: 41448

American (AMR) AF: 0.267 AC: 4083 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 922 AN: 3470

East Asian (EAS) AF: 0.359 AC: 1852 AN: 5164

South Asian (SAS) AF: 0.315 AC: 1519 AN: 4818

European-Finnish (FIN) AF: 0.208 AC: 2204 AN: 10578

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18488 AN: 67964

Other (OTH) AF: 0.303 AC: 640 AN: 2110

Alfa AF: 0.279 Hom.: 24996

Bravo AF: 0.304

Asia WGS AF: 0.346 AC: 1199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	2.8
DANN	Benign	0.57
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;