7-55212052-A-G

Variant names:

• chr7-55212052-A-G
• rs940806
• ENST00000836806.1:n.207+711T>C

Variant summary

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

The ENST00000836806.1(EGFR-AS1):​n.207+711T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 152,128 control chromosomes in the GnomAD database, including 34,354 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 0.66 (34354 hom., cov: 33)
• Consequence: EGFR-AS1 ENST00000836806.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860
• Publications: 14 publications found

Genes affected

EGFR-AS1 (HGNC:40207): (EGFR antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836806.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EGFR-AS1	ENST00000836806.1		n.207+711T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100562 AN: 152010 Hom.: 34296 Cov.: 33

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.662 AC: 100677 AN: 152128 Hom.: 34354 Cov.: 33 AF XY: 0.666 AC XY: 49549 AN XY: 74356

African (AFR) AF: 0.794 AC: 32961 AN: 41526

American (AMR) AF: 0.684 AC: 10452 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1890 AN: 3468

East Asian (EAS) AF: 0.880 AC: 4559 AN: 5178

South Asian (SAS) AF: 0.800 AC: 3860 AN: 4828

European-Finnish (FIN) AF: 0.548 AC: 5788 AN: 10562

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39086 AN: 67964

Other (OTH) AF: 0.649 AC: 1373 AN: 2116

Alfa AF: 0.602 Hom.: 45916

Bravo AF: 0.679

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.61
PhyloP100		-0.086
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs940806; hg19: chr7-55279745;