rs1107618

Variant names:

• chr7-55212590-G-A
• rs1107618
• ENST00000836806.1:n.207+173C>T

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+173C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,136 control chromosomes in the GnomAD database, including 11,645 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 0.35 (11645 hom., cov: 33)
• Consequence: EGFR-AS1 ENST00000836806.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• Publications: 3 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EGFR-AS1	ENST00000836806.1	n.207+173C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52800 AN: 152018 Hom.: 11623 Cov.: 33

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.348 AC: 52874 AN: 152136 Hom.: 11645 Cov.: 33 AF XY: 0.357 AC XY: 26566 AN XY: 74362

African (AFR) AF: 0.577 AC: 23933 AN: 41502

American (AMR) AF: 0.291 AC: 4445 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3468

East Asian (EAS) AF: 0.754 AC: 3900 AN: 5170

South Asian (SAS) AF: 0.439 AC: 2119 AN: 4824

European-Finnish (FIN) AF: 0.303 AC: 3204 AN: 10570

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13774 AN: 67996

Other (OTH) AF: 0.313 AC: 662 AN: 2114

Alfa AF: 0.239 Hom.: 4982

Bravo AF: 0.359

Asia WGS AF: 0.579 AC: 2012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.54
PhyloP100		-2.1
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: rs1107618; hg19: chr7-55280283;