rs6782264

Variant names:

• chr3-168534516-C-T
• rs6782264
• ENST00000431685.2:n.424-110733C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000431685.2(EGFEM1P):​n.424-110733C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0224 in 151,996 control chromosomes in the GnomAD database, including 58 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 0.022 (58 hom., cov: 32)
• Consequence: EGFEM1P ENST00000431685.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 1 publications found

Genes affected

EGFEM1P (HGNC:25149): (EGF like and EMI domain containing 1, pseudogene)

ENSG00000293389 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0224 (3402/151996) while in subpopulation AFR AF = 0.0516 (2139/41474). AF 95% confidence interval is 0.0498. There are 58 homozygotes in GnomAd4. There are 1587 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 58 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EGFEM1P	NR_021485.2	n.852+14876C>T		intron_variant	Intron 4 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EGFEM1P	ENST00000431685.2	n.424-110733C>T		intron_variant	Intron 4 of 11	6
ENSG00000293389	ENST00000506760.3	n.105+14876C>T		intron_variant	Intron 1 of 9	5
ENSG00000293389	ENST00000832671.1	n.105+14876C>T		intron_variant	Intron 1 of 10

Frequencies

GnomAD3 genomes AF: 0.0224 AC: 3405 AN: 151878 Hom.: 58 Cov.: 32

Gnomad AFR AF: 0.0518

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.00959

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000622

Gnomad FIN AF: 0.00256

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0154

Gnomad OTH AF: 0.0139

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0224 AC: 3402 AN: 151996 Hom.: 58 Cov.: 32 AF XY: 0.0214 AC XY: 1587 AN XY: 74288

African (AFR) AF: 0.0516 AC: 2139 AN: 41474

American (AMR) AF: 0.00958 AC: 146 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.000622 AC: 3 AN: 4822

European-Finnish (FIN) AF: 0.00256 AC: 27 AN: 10554

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0154 AC: 1045 AN: 67952

Other (OTH) AF: 0.0138 AC: 29 AN: 2106

Alfa AF: 0.0183 Hom.: 5

Bravo AF: 0.0242

Asia WGS AF: 0.00320 AC: 11 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.8
DANN	Benign	0.56
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs6782264; hg19: chr3-168252304;