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 ENST00000808839.1(ENSG00000305114):​n.567A>C 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: ENSG00000305114 ENST00000808839.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808839.1. 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.151T>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000305114	ENST00000808839.1		n.567A>C		non_coding_transcript_exon	Exon 4 of 5
	ENSG00000305114	ENST00000808841.1		n.520A>C		non_coding_transcript_exon	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 v4.9

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;