7-55212575-A-C

Variant names:

• chr7-55212575-A-C
• rs1107617
• ENST00000836806.1:n.207+188T>G

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+188T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,270 control chromosomes in the GnomAD database, including 1,918 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 0.13 (1918 hom., cov: 34)
• Consequence: EGFR-AS1 ENST00000836806.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 7 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 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+188T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20487 AN: 152152 Hom.: 1913 Cov.: 34

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.0964

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0902

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.135 AC: 20521 AN: 152270 Hom.: 1918 Cov.: 34 AF XY: 0.138 AC XY: 10278 AN XY: 74454

African (AFR) AF: 0.181 AC: 7535 AN: 41554

American (AMR) AF: 0.114 AC: 1739 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0807 AC: 280 AN: 3470

East Asian (EAS) AF: 0.469 AC: 2423 AN: 5162

South Asian (SAS) AF: 0.200 AC: 963 AN: 4826

European-Finnish (FIN) AF: 0.0964 AC: 1023 AN: 10616

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0902 AC: 6138 AN: 68016

Other (OTH) AF: 0.134 AC: 283 AN: 2114

Alfa AF: 0.110 Hom.: 3855

Bravo AF: 0.142

Asia WGS AF: 0.282 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.3
DANN	Benign	0.35
PhyloP100		0.50
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: rs1107617; hg19: chr7-55280268;