rs6782264

chr3-168534516-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_021485.2(EGFEM1P):n.852+14876C>T variant causes a intron, non coding transcript 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 NR_021485.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 58 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EGFEM1P	NR_021485.2	n.852+14876C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EGFEM1P	ENST00000431685.2	n.424-110733C>T		intron_variant, non_coding_transcript_variant
	ENST00000506760.2	n.34+14876C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.0516

Gnomad4 AMR AF: 0.00958

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000622

Gnomad4 FIN AF: 0.00256

Gnomad4 NFE AF: 0.0154

Gnomad4 OTH AF: 0.0138

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6782264; hg19: chr3-168252304;